The calculations were made in R using R-Studio. The structure of the
code is essentially based on the structure of the text. The raw code is
in the file order_of_code.R. The file extended with
Markdown is order_of_code-doc.RMD and the file
order_of_code-doc.html is generated from it.
Note: The base path for rmd files is the folder in which they are
located, not the r-project. Consequently, order_of_code.R
and order_of_code-doc.RMD are both located in the root
folder of the project.
Depending on the hardware, the subsequent code can run for several hours or even a few days.
Install “Just Another Gibbs Sampler” (JAGS) (Plummer, 2003) if you want to run the Bayesian analyses anew. Version 4.3 - as used here - can be downloaded in pre-compiled form for a number of OS here: https://sourceforge.net/projects/mcmc-jags/ . The manual can be found here: https://people.stat.sc.edu/hansont/stat740/jags_user_manual.pdf
The code makes extensive use of the function source to
call external code. Thus, the main part of the code remains slim, well
structured and readable.
Install required packages, set some options and link the sources for the helper functions.
Remark: Depending on your R version the package osmplotr may be
installed from github using
devtools::install_github ("ropensci/osmplotr").
require(pacman) || install.packages("pacman")
## Loading required package: pacman
## [1] TRUE
pacman::p_load(coda, cowplot, demogR, dplyr, flexsurv, ggplot2, ggrepel, grid,
gridExtra, HMDHFDplus, kableExtra, Metrics, mortAAR, osmdata,
psych, readxl, reshape2, rjags, runjags, sf, tidyr, ggspatial)
options(scipen = 999)
options(dplyr.summarise.inform = FALSE)
source("./functions/gomp_MLE.R")
source("./functions/gomp_MLE_adapted.R")
source("./functions/gomp_MLE_interval.R")
source("./functions/gomp_anthr_age.R")
source("./functions/gomp_anthr_age_r.R")
source("./functions/gomp_known_age.R")
source("./functions/gomp_known_age_r.R")
source("./functions/helper_functions.R")
source("./functions/lt_MC.R")
source("./functions/lt_MC_Gomp.R")
RNGkind("L'Ecuyer-CMRG") # conservative random number generator to avoid periodicity
Important for saving time: Decide to run extensive code anew (app. 6 h +). In addition, you can set the folder for preprocessed files.
runCodeNew <- FALSE
#runCodeNew <- TRUE
# Ask for credentials of the Human Mortality Database if the code runs anew
if (runCodeNew){
HMD_username <- readline(prompt = "Enter username: ")
HMD_password <- readline(prompt="Enter password: ")
credentials <- c(HMD_username, HMD_password)
}
# Specify filename prefix for saved files and create a folder if needed:
saveFileDir = "preprocessed_files"
if (saveFileDir %in% list.files(getwd())) {
# Dir exists
}else{
dir.create(file.path(".", saveFileDir), showWarnings = FALSE )
}
## NULL
# beta model values
beta1 <- 0.025
beta2 <- 0.04
beta3 <- 0.06
beta4 <- 0.09
# hgompertz(x, shape, rate):
# x = age, shape = beta value, rate = derived from Sasaki & Kondo 2016 fig. 1, 2
# rate values according Sasaki & Kondo 2016 fig. 1, line 6, 30
Sab <- -2.624
Sbb <- 0.0393
Ma <- -7.119
Mb <- 0.0718
M1 <- Sab * (beta1 - Mb) / Sbb + Ma
M2 <- Sab * (beta2 - Mb) / Sbb + Ma
M3 <- Sab * (beta3 - Mb) / Sbb + Ma
M4 <- Sab * (beta4 - Mb) / Sbb + Ma
gridExtra::grid.arrange (
ggplot() + xlim(15, 100) + ylim(0, 0.4) +
geom_function(fun = function(x) flexsurv::hgompertz(x - 15, 0.025, exp(M1)),
aes(col = "\u03B2 = 0.025")) +
geom_function(fun = function(x) flexsurv::hgompertz(x - 15, 0.04, exp(M2)),
aes(col = "\u03B2 = 0.04")) +
geom_function(fun = function(x) flexsurv::hgompertz(x - 15, 0.06, exp(M3)),
aes(col = "\u03B2 = 0.06")) +
geom_function(fun = function(x) flexsurv::hgompertz(x - 15, 0.09, exp(M4)),
aes(col = "\u03B2 = 0.9")) +
ylab("hazard") + xlab("age in years") +
theme_light() +
scale_colour_manual(values = c("red","blue","green", "dark grey")) +
theme(legend.position = c(0.2, 0.7), legend.title = element_blank()),
ggplot() + xlim(15, 105) +
geom_function(fun = function(x) log(flexsurv::hgompertz(x - 15, 0.025, exp(M1))), colour = "red") +
geom_function(fun = function(x) log(flexsurv::hgompertz(x - 15, 0.04, exp(M2))), colour= "blue") +
geom_function(fun = function(x) log(flexsurv::hgompertz(x - 15, 0.06, exp(M3))), colour= "green") +
geom_function(fun = function(x) log(flexsurv::hgompertz(x - 15, 0.09, exp(M4))), colour= "dark grey") +
xlab("age in years") + ylab("hazard (log scale)") +
theme_light(),
ggplot() + xlim(15, 105) +
geom_function(fun = function(x) flexsurv::dgompertz(x - 15, 0.025, exp(M1)), colour = "red") +
geom_function(fun = function(x) flexsurv::dgompertz(x - 15, 0.04, exp(M2)), colour= "blue") +
geom_function(fun = function(x) flexsurv::dgompertz(x - 15, 0.06, exp(M3)), colour= "green") +
geom_function(fun = function(x) flexsurv::dgompertz(x - 15, 0.09, exp(M4)), colour= "dark grey") +
xlab("age in years") + ylab("density") +
theme_light(),
# gomp_lx() s. functions\helper_functions.R
ggplot() + xlim(15, 105) + ylim(0, 1) +
geom_function(fun = function(x) gomp_lx(x - 15, exp(M1), 0.025), colour = "red") +
geom_function(fun = function(x) gomp_lx(x - 15, exp(M2), 0.04), colour = "blue") +
geom_function(fun = function(x) gomp_lx(x - 15, exp(M3), 0.06), colour = "green") +
geom_function(fun = function(x) gomp_lx(x - 15, exp(M4), 0.09), colour = "dark grey") +
ylab("survival") + xlab("age in years") +
theme_light(),
ncol = 2
) -> gompertz_plot
# Save the finished map object
ggsave(
filename = "fig01_gompertz_plot.pdf",
width = 8, height = 6,
plot = gompertz_plot,
device = cairo_pdf,
path = "documented"
)
# Login needed to retrieve data from the Human Mortality Database
# https://mortality.org/
if (runCodeNew){
login <- askYesNo(paste("Login for Human Mortality Database needed.",
"Do you want to proceed?", sep = "\n"),
default = FALSE)
# get dx
if (login){
HMD_UK_result_1_year <- HMDHFDplus::readHMDweb("GBRTENW", "bltper_1x1",
credentials[1],
credentials[2])
# saves results in Rda-object
save(HMD_UK_result_1_year, file = file.path(".", saveFileDir, "HMD_UK_result_1_year.Rda") )
}
} else {load(file.path(".", saveFileDir, "HMD_UK_result_1_year.Rda") )
}
gridExtra::grid.arrange(
ggplot(HMD_UK_result_1_year[which(HMD_UK_result_1_year$Year == 1841),]) +
geom_line(aes(x = Age, y = mx)) +
scale_y_continuous(trans='log10') + labs(y = expression(m[x] * " (log scale)")) +
annotate("rect", xmin = 7, xmax = 17, ymin = 0.004, ymax = 0.01,
alpha = .1,fill = "blue") +
annotate (geom = "text", x = 12, y = 0.012, label = "zoom") +
theme_light(),
ggplot(HMD_UK_result_1_year[which(HMD_UK_result_1_year$Year == 1841),],
aes(x = Age, y = mx)) + scale_x_continuous(breaks=seq(8,16,2), limits=c(7, 17)) +
geom_line() + geom_point() +
ylim(0.004, 0.01) +
labs(y = expression(m[x]))+
annotate (geom = "text", x = 10, y = 0.009, label = "zoomed in") +
geom_segment(aes(x = 12, y = 0.007, xend = 12, yend = 0.0055),
arrow = arrow(length = unit(0.25, "cm")), colour = "red") +
theme_light(),
ncol = 1
) -> HMD_UK_hazard_plot
# Save the finished map object
ggsave(
filename = "fig03_HMD_UK_hazard_plot.pdf",
plot = HMD_UK_hazard_plot,
device = "pdf",
path = "documented"
)
## Saving 7 x 5 in image
# Get the coordinates of sites to be plotted
sites_data <- rbind.data.frame(
c("1","Bermondsey Abbey", 51.4975,-0.080833),
c("2", "St Mary Spital", 51.518716, -0.079161),
c("3","St Mary Graces",51.509289,-0.072916 ),
c("4", "New Churchyard", 51.517403, -0.084216),
c("5","St Benet Sherehog",51.513194,-0.091389),
c("6", "Chelsea Old Church", 51.483222, -0.170795),
c("7","St Bride's crypt",51.513802,-0.105292),
c("8", "St Bride's lower churchyard", 51.515253, -0.104973),
c("9", "Sheen's burial ground", 51.51480, -0.06760),
c("10","St Marylebone", 51.5225,-0.152222),
c("11",paste("St Marylebone's Paddington", "Street north", sep="\n"), 51.520869, -0.154515),
c("12", "Bow Baptist church", 51.529540, -0.01580),
c("13", "St Mary and St Michael", 51.51330, -0.05190)
)
colnames(sites_data) <-c("nr", "name", "lat", "lon")
sites_data$lat<-as.numeric(sites_data$lat)
sites_data$lon<-as.numeric(sites_data$lon)
dat_sites <- st_as_sf(sites_data,
coords = c("lon", "lat"),
crs = 4326)
# Build a bounding box by the coordinates + 10% of the extent as frame
bbox <- matrix(
c(
min(sites_data$lon) - (0.1*(max(sites_data$lon)- min(sites_data$lon))),
min(sites_data$lat) - (0.1*(max(sites_data$lat)- min(sites_data$lat))),
max(sites_data$lon) + (0.1*(max(sites_data$lon)- min(sites_data$lon))),
max(sites_data$lat) + (0.1*(max(sites_data$lat)- min(sites_data$lat)))
),
byrow = FALSE, nrow = 2, ncol = 2,
dimnames = list(c('x','y'),c('min','max'))
)
# Querry the osm data
# If the bbox has been changed please run the statement to get the new osm data.
if (!exists ("q_admin8") | (runCodeNew == TRUE)) {
q_admin8 <- bbox %>% opq() %>%
add_osm_feature(key = "boundary", value = "administrative") %>%
add_osm_feature(key = "admin_level", value = "8") %>%
osmdata_sf()
}
# Build the map
London_map <- ggplot() +
geom_sf(data = q_admin8$osm_multipolygons, fill=rgb(0.9,0.9,0.9)) +
geom_sf_text(data = q_admin8$osm_multipolygons, aes(label=sub('.*of ','',name)), size=3) +
geom_sf(data = dat_sites,aes(), shape = 16, colour = "black", size = 2) +
ggrepel::geom_label_repel(data = dat_sites, aes(label = nr, geometry = geometry),
stat = "sf_coordinates", min.segment.length = 0, size=4) +
annotate("label", x = -0.28, y = 51.38, hjust = 0, vjust = 0, size = 3,
label = paste(apply(sites_data[1:6,1:2],1,paste,collapse = ": "),
collapse = "\n")) +
annotate("label", x = -0.12, y = 51.38, hjust = 0, vjust = 0, size = 3,
label = paste(apply(sites_data[7:13,1:2],1,paste,collapse = ": "),
collapse = "\n")) +
xlim (-0.28, 0.03) +
ylim (51.38,51.58) +
theme_light() +
theme(panel.grid = element_blank()) +
theme(axis.title = element_blank()) +
ggspatial::annotation_scale(location = 'tl', height= unit(0.15, "cm"))
plot(London_map)
# Save the finished map object
ggsave(
filename = "fig04_london_map.pdf",
plot = London_map,
device = "pdf",
path = "documented"
)
## Saving 7 x 5 in image
read.table("chapter_03_data/london_cemeteries.txt", header = T, sep = "\t") %>%
knitr::kable(., col.names = c("Map no.", "Name", "Period", "Excavation year", "Social character", "Absolute n", "n analysed", "n >= 12 years", "References")) %>%
kableExtra::kable_styling(latex_options = "HOLD_position") %>% unclass() %>% cat()
| Map no. | Name | Period | Excavation year | Social character | Absolute n | n analysed | n >= 12 years | References |
|---|---|---|---|---|---|---|---|---|
| 1 | Bermondsey Abbey | 1089–1538 | 1984–1995 | monks | 208 | 201 | 201 | Dyson, Samuel, Steele, & Wright (2011) |
| 2 | St Mary Spital | 1120–1538 | 1991–2007 | commoners | 10,516 | 5,387 | Connell, Gray Jones, Redfern, & Walker (2012) | |
| NA | period 14: 1120–1200 | 347 | 329 | |||||
| NA | period 15: 1200–1250 | 510 | 470 | |||||
| NA | period 16: 1250–1400 | 1,392 | 1,361 | |||||
| NA | period 17: 1400–1539 | 526 | 467 | |||||
| 3 | St Mary Graces | 1350–1540 | 1986–1988 | commoners | 378 | 298 | Grainger & Phillpotts (2011) | |
| 4 | New Churchyard | 1569–1739 | 2011–2015 | low status | 3,354 | 682 (category A) | 556 | Hartle, Carty, Henderson, Knox, & Walker (2017) |
| 5 | St Benet Sherehog | 1670–1740 | 1994–1996 | higher status | 230 | 179 | Miles, White, & Tankard (2008) | |
| 6 | Chelsea Old church | 1712–1842 | 2000 | mixed | 198 | 168 | Cowie, Bekvalac, & Kausmally (2008) | |
| 7 | St Brides crypt | 1740–1853 | high | 216 | J. L. Scheuer (1995); L. Scheuer (1998) | |||
| 8 | St Brides lower churchyard | 1770–1849 | low | 606 | 379 | Kausmally (2008) | ||
| 9 | Sheens burial ground | 1763–1853 | 2006–2007 | low | 265 | 254 | 172 | Henderson, Miles, & Walker (2013) |
| 10 | St Marylebone | 1767–1859 | 1992; 2003 | high status | 301 | 226 | Miles, Powers, Wroe-Brown, & Walker (2008) | |
| 11 | St Marylebone Paddington Street north | 1772–1853 | 2012–2013 | high status | 385 | 291 | 232 | Henderson, Walker, & Miles (2015) |
| 12 | Bow Baptist church | 1816–1853 | 2006; 2008 | villagers | 440 | 416 | 231 | Henderson et al. (2013) |
| 13 | St Mary and St Michaels burial ground | 1843–1854 | 2004–2005 | low, Irish immigrants | 760 | 705 | 284 | Henderson et al. (2013) |
source("./chapter_03_data/London_population.R")
grid::grid.newpage()
grid::grid.draw(rbind(london_pop1, london_pop2))
Calculated in ./chapter_03_data/London_population.R
knitr::kable(razz_df)%>%
kableExtra::kable_styling(latex_options = "HOLD_position")
| date | population | rate.per.year |
|---|---|---|
| 1520 | 55000 | NA |
| 1600 | 200000 | 0.016 |
| 1650 | 400000 | 0.014 |
| 1700 | 575000 | 0.007 |
| 1750 | 675000 | 0.003 |
| 1801 | 960000 | 0.007 |
| 1851 | 2685000 | 0.021 |
Preprocessing of data used in figure 6: Estimated modal ages.
The data is referenced and aggregated in
“./chapter_04_results/historical_lifetables.R”. In this file, all
records from individual preprocessing files located in
“./liftables_preprocessed/” are sourced. The corresponding
data files are stored in “./data/”.
London_1728_1840.R, Mortality_bills_1728_1840.txt, Source: Roberts & Cox (2003), 304 Table 6.5; > 100 years and < 1 year collapsed
source("./chapter_04_results/historical_lifetables.R")
kable(london_1728_1840_ranges,
caption = "London Mortality bills 1728-1840.") %>%
kableExtra::kable_styling(latex_options = "HOLD_position")
| parameter | ranges |
|---|---|
| beta | 0.0324-0.0419 |
| M | 43.4-54.8 |
kable(london_1728_1840_ranges_r,
caption = "London Mortality bills 1728-1840, corrected for population growth.") %>%
kableExtra::kable_styling(latex_options = "HOLD_position")
| parameter | ranges |
|---|---|
| beta_r | 0.0327-0.0501 |
| M_r | 45.1-64.4 |
| r | 0.002-0.019 |
London_1841_raw_all.R, London_1841_raw.txt, Source: Graham (1842), 19 table q.
kable(London_1841_ranges,
caption = "Census data for London from 1841.") %>%
kableExtra::kable_styling(latex_options = "HOLD_position")
| parameter | modes | HDI.ranges |
|---|---|---|
| beta | 0.0547 | 0.0510-0.0585 |
| M | 60.4164 | 58.9-61.7 |
English_Mortality.R, wrigley_et_al_1997_england_1640-1809.txt, Source: Wrigley, Oeppen, Davies, & Schofield (1997), 290 table 6.19
kable(eng_mort_ranges,
caption = "English mortality data.") %>%
kableExtra::kable_styling(latex_options = "HOLD_position")
| parameter | ranges |
|---|---|
| beta | 0.0438-0.0608 |
| M | 52.2-67.4 |
HMD_UK_ranges.R
The data from the Human Mortality Database (https://mortality.org/) were retrieved with a personal account using the R package HMDHFDplus. Therefore, we only provide the processed data here.
kable(HMD_UK_ranges, caption = "Human Mortality Database UK.") %>%
kableExtra::kable_styling(latex_options = "HOLD_position")
| parameter | ranges |
|---|---|
| beta | 0.05-0.0654 |
| M | 64.2-70.2 |
English_Peers.R, russell.txt, Source: La Poutré & Janssen (2021), table 2
kable(peers_ranges, caption = "English Peers") %>%
kableExtra::kable_styling(latex_options = "HOLD_position")
| parameter | modes | HDI.ranges |
|---|---|---|
| beta | 0.0613 | 0.0559-0.0660 |
| M | 58.1758 | 56.4-59.8 |
| e20 | 33.4148 | NA |
| e25 | 29.4926 | NA |
Medieval_England.R, Christ_church_monks.txt, Source: Hatcher, Piper, & Stone (2006), 28 table 2
kable(monks_ranges, caption = "Christ Church monks") %>%
kableExtra::kable_styling(latex_options = "HOLD_position")
| parameter | modes | HDI.ranges |
|---|---|---|
| beta | 0.0461 | 0.0398-0.0523 |
| M | 52.7659 | 48.9-56.0 |
| e20 | 31.0948 | NA |
| e25 | 27.7530 | NA |
kable(london_1728_1840_result,
caption = "London Mortality bills 1728-1840.") %>%
kableExtra::kable_styling(latex_options = c("HOLD_position","scale_down"))
| year | parameter | PSRF Point est. | PSRF Upper C.I. | Mean | Median | Mode | ESS | MCSE | HDImass | HDIlow | HDIhigh |
|---|---|---|---|---|---|---|---|---|---|---|---|
| X1728 | alpha | 1.000108 | 1.000395 | 0.0146970 | 0.0146465 | 0.0145984 | 16365.6 | 0.0000105 | 0.95 | 0.0121552 | 0.0173894 |
| X1728 | beta | 1.000120 | 1.000451 | 0.0349080 | 0.0349052 | 0.0347825 | 16828.8 | 0.0000207 | 0.95 | 0.0296327 | 0.0401025 |
| X1728 | M | 1.000140 | 1.000453 | 44.6140062 | 44.8625026 | 45.0618057 | 16114.3 | 0.0233898 | 0.95 | 38.7086866 | 50.1735217 |
| X1730 | alpha | 1.000025 | 1.000130 | 0.0156646 | 0.0156056 | 0.0154789 | 18337.2 | 0.0000111 | 0.95 | 0.0127633 | 0.0186414 |
| X1730 | beta | 1.000039 | 1.000168 | 0.0325426 | 0.0325361 | 0.0324144 | 18117.0 | 0.0000207 | 0.95 | 0.0270931 | 0.0379764 |
| X1730 | M | 1.000030 | 1.000142 | 42.2093093 | 42.5573739 | 43.4233691 | 18020.2 | 0.0277785 | 0.95 | 34.7516415 | 49.0050848 |
| X1740 | alpha | 1.000112 | 1.000403 | 0.0153878 | 0.0153418 | 0.0152749 | 17990.7 | 0.0000100 | 0.95 | 0.0128087 | 0.0180175 |
| X1740 | beta | 1.000101 | 1.000385 | 0.0337646 | 0.0337606 | 0.0335736 | 17926.6 | 0.0000190 | 0.95 | 0.0288006 | 0.0387511 |
| X1740 | M | 1.000157 | 1.000484 | 43.0932517 | 43.3416150 | 44.0450446 | 17518.4 | 0.0233112 | 0.95 | 36.9618783 | 48.8486639 |
| X1750 | alpha | 1.000308 | 1.001170 | 0.0151942 | 0.0151449 | 0.0150989 | 18259.5 | 0.0000101 | 0.95 | 0.0125952 | 0.0179004 |
| X1750 | beta | 1.000351 | 1.001292 | 0.0342717 | 0.0342730 | 0.0342242 | 18121.9 | 0.0000195 | 0.95 | 0.0290667 | 0.0393662 |
| X1750 | M | 1.000317 | 1.001174 | 43.5548106 | 43.8136623 | 44.5458564 | 17813.4 | 0.0230371 | 0.95 | 37.3772875 | 49.2243556 |
| X1760 | alpha | 1.000338 | 1.000801 | 0.0145711 | 0.0145269 | 0.0143509 | 17449.6 | 0.0000100 | 0.95 | 0.0120404 | 0.0171711 |
| X1760 | beta | 1.000241 | 1.000520 | 0.0350287 | 0.0350196 | 0.0349168 | 17085.2 | 0.0000201 | 0.95 | 0.0299236 | 0.0402371 |
| X1760 | M | 1.000363 | 1.000866 | 44.8827829 | 45.1095653 | 45.6086874 | 17106.4 | 0.0221726 | 0.95 | 39.1055721 | 50.2653901 |
| X1770 | alpha | 1.000175 | 1.000588 | 0.0143221 | 0.0142774 | 0.0142718 | 17407.1 | 0.0000099 | 0.95 | 0.0117796 | 0.0169045 |
| X1770 | beta | 1.000110 | 1.000381 | 0.0355969 | 0.0356004 | 0.0358743 | 17291.4 | 0.0000203 | 0.95 | 0.0304311 | 0.0408902 |
| X1770 | M | 1.000178 | 1.000591 | 45.4300281 | 45.6462299 | 45.7955369 | 17214.1 | 0.0214852 | 0.95 | 39.8417826 | 50.7260430 |
| X1780 | alpha | 1.000269 | 1.000935 | 0.0136238 | 0.0135783 | 0.0135358 | 16804.1 | 0.0000095 | 0.95 | 0.0112248 | 0.0160214 |
| X1780 | beta | 1.000239 | 1.000906 | 0.0367220 | 0.0367253 | 0.0367228 | 16729.5 | 0.0000201 | 0.95 | 0.0317062 | 0.0419311 |
| X1780 | M | 1.000314 | 1.001006 | 46.8874156 | 47.0760558 | 47.5932925 | 16847.5 | 0.0195467 | 0.95 | 41.7873949 | 51.6004245 |
| X1790 | alpha | 1.000213 | 1.000318 | 0.0126517 | 0.0126141 | 0.0126627 | 16987.5 | 0.0000089 | 0.95 | 0.0103904 | 0.0149291 |
| X1790 | beta | 1.000153 | 1.000189 | 0.0385170 | 0.0385078 | 0.0385633 | 16735.7 | 0.0000203 | 0.95 | 0.0333069 | 0.0435894 |
| X1790 | M | 1.000247 | 1.000390 | 48.8232330 | 48.9686652 | 49.3336238 | 17313.3 | 0.0172234 | 0.95 | 44.3303384 | 53.1112910 |
| X1800 | alpha | 1.000066 | 1.000135 | 0.0116898 | 0.0116448 | 0.0115679 | 15913.4 | 0.0000085 | 0.95 | 0.0096159 | 0.0138219 |
| X1800 | beta | 1.000108 | 1.000229 | 0.0399437 | 0.0399437 | 0.0398114 | 16280.5 | 0.0000202 | 0.95 | 0.0348971 | 0.0449998 |
| X1800 | M | 1.000048 | 1.000103 | 50.7070955 | 50.8409969 | 51.0720614 | 16902.5 | 0.0156219 | 0.95 | 46.6498010 | 54.5415198 |
| X1810 | alpha | 1.000554 | 1.001977 | 0.0115040 | 0.0114672 | 0.0113409 | 15693.3 | 0.0000082 | 0.95 | 0.0095496 | 0.0135586 |
| X1810 | beta | 1.000705 | 1.002539 | 0.0384284 | 0.0384204 | 0.0384387 | 15514.8 | 0.0000196 | 0.95 | 0.0336019 | 0.0431446 |
| X1810 | M | 1.000514 | 1.001824 | 51.3269015 | 51.4533360 | 51.7564282 | 16513.8 | 0.0160886 | 0.95 | 47.1307998 | 55.1816194 |
| X1820 | alpha | 1.000033 | 1.000085 | 0.0104903 | 0.0104573 | 0.0103834 | 15105.4 | 0.0000079 | 0.95 | 0.0086455 | 0.0124121 |
| X1820 | beta | 1.000043 | 1.000117 | 0.0403661 | 0.0403518 | 0.0400258 | 14941.4 | 0.0000204 | 0.95 | 0.0354922 | 0.0452322 |
| X1820 | M | 1.000026 | 1.000068 | 53.3477816 | 53.4500376 | 53.7200147 | 16242.5 | 0.0145904 | 0.95 | 49.6159817 | 56.8461806 |
| X1830 | alpha | 1.000262 | 1.000742 | 0.0098565 | 0.0098250 | 0.0097444 | 14287.5 | 0.0000077 | 0.95 | 0.0080915 | 0.0116937 |
| X1830 | beta | 1.000328 | 1.000824 | 0.0420331 | 0.0420192 | 0.0419423 | 14811.9 | 0.0000207 | 0.95 | 0.0371686 | 0.0470269 |
| X1830 | M | 1.000204 | 1.000597 | 54.4845443 | 54.5690888 | 54.8316675 | 16013.8 | 0.0134579 | 0.95 | 51.1240793 | 57.7697242 |
| X1840 | alpha | 1.000065 | 1.000175 | 0.0103000 | 0.0102638 | 0.0101621 | 14542.4 | 0.0000080 | 0.95 | 0.0084719 | 0.0122192 |
| X1840 | beta | 1.000062 | 1.000189 | 0.0409226 | 0.0409164 | 0.0407728 | 14161.3 | 0.0000212 | 0.95 | 0.0360077 | 0.0458839 |
| X1840 | M | 1.000053 | 1.000143 | 53.6798657 | 53.7773975 | 53.7555529 | 15909.8 | 0.0144310 | 0.95 | 50.0411401 | 57.1294679 |
kable(london_1728_1840_result_r,
caption = "London Mortality bills 1728-1840, corrected for population growth.") %>%
kableExtra::kable_styling(latex_options = c("HOLD_position","scale_down"))
| year | parameter | PSRF Point est. | PSRF Upper C.I. | Mean | Median | Mode | ESS | MCSE | HDImass | HDIlow | HDIhigh |
|---|---|---|---|---|---|---|---|---|---|---|---|
| X1728 | alpha | 1.000493 | 1.001271 | 0.0120388 | 0.0119639 | 0.0117705 | 13219.2 | 0.0000127 | 0.95 | 0.0092381 | 0.0149068 |
| X1728 | beta | 1.000293 | 1.000781 | 0.0373256 | 0.0373497 | 0.0374499 | 14626.6 | 0.0000261 | 0.95 | 0.0312018 | 0.0435282 |
| X1728 | M | 1.000607 | 1.001494 | 50.2038587 | 50.4495217 | 50.9806000 | 13687.7 | 0.0264982 | 0.95 | 43.9280763 | 55.9188957 |
| X1728 | rate | 1.000147 | 1.000459 | 0.0066686 | 0.0066694 | 0.0067571 | 27227.8 | 0.0000151 | 0.95 | 0.0018302 | 0.0116186 |
| X1730 | alpha | 1.000269 | 1.000770 | 0.0148858 | 0.0147951 | 0.0145680 | 14694.8 | 0.0000148 | 0.95 | 0.0115075 | 0.0185145 |
| X1730 | beta | 1.000150 | 1.000455 | 0.0324320 | 0.0324651 | 0.0327068 | 16554.5 | 0.0000253 | 0.95 | 0.0260065 | 0.0387515 |
| X1730 | M | 1.000349 | 1.000914 | 43.6813384 | 44.1622266 | 45.0521696 | 14720.2 | 0.0375115 | 0.95 | 34.6717649 | 52.0836240 |
| X1730 | rate | 1.000125 | 1.000492 | 0.0017597 | 0.0017647 | 0.0017560 | 31387.5 | 0.0000140 | 0.95 | -0.0031019 | 0.0066355 |
| X1740 | alpha | 1.000329 | 1.000720 | 0.0146610 | 0.0145783 | 0.0142673 | 12838.5 | 0.0000145 | 0.95 | 0.0115556 | 0.0179785 |
| X1740 | beta | 1.000371 | 1.001036 | 0.0338783 | 0.0339015 | 0.0340453 | 14559.4 | 0.0000244 | 0.95 | 0.0281672 | 0.0397172 |
| X1740 | M | 1.000313 | 1.000633 | 44.5110399 | 44.8625313 | 45.6855802 | 12927.7 | 0.0334910 | 0.95 | 36.8686339 | 51.5460098 |
| X1740 | rate | 1.000079 | 1.000225 | 0.0015451 | 0.0015464 | 0.0015893 | 25927.1 | 0.0000155 | 0.95 | -0.0033455 | 0.0064169 |
| X1750 | alpha | 1.000091 | 1.000301 | 0.0126650 | 0.0125920 | 0.0124096 | 13381.2 | 0.0000131 | 0.95 | 0.0097778 | 0.0156841 |
| X1750 | beta | 1.000158 | 1.000520 | 0.0363874 | 0.0364000 | 0.0364127 | 15055.2 | 0.0000254 | 0.95 | 0.0303579 | 0.0425971 |
| X1750 | M | 1.000109 | 1.000338 | 48.8679712 | 49.1288156 | 49.6582623 | 13657.6 | 0.0280568 | 0.95 | 42.3123463 | 55.0499366 |
| X1750 | rate | 1.000002 | 1.000003 | 0.0061501 | 0.0061570 | 0.0061586 | 28511.9 | 0.0000148 | 0.95 | 0.0012302 | 0.0110002 |
| X1760 | alpha | 1.000046 | 1.000138 | 0.0118787 | 0.0118090 | 0.0117666 | 13167.5 | 0.0000125 | 0.95 | 0.0091035 | 0.0146849 |
| X1760 | beta | 1.000017 | 1.000101 | 0.0375028 | 0.0375223 | 0.0376118 | 15087.9 | 0.0000254 | 0.95 | 0.0314240 | 0.0436194 |
| X1760 | M | 1.000075 | 1.000168 | 50.5533524 | 50.7836185 | 51.6251396 | 13738.2 | 0.0259954 | 0.95 | 44.4208165 | 56.2002552 |
| X1760 | rate | 1.000014 | 1.000079 | 0.0068523 | 0.0068519 | 0.0068244 | 26661.9 | 0.0000153 | 0.95 | 0.0019504 | 0.0117469 |
| X1770 | alpha | 1.000380 | 1.001203 | 0.0121911 | 0.0121201 | 0.0120472 | 13162.6 | 0.0000128 | 0.95 | 0.0093360 | 0.0150793 |
| X1770 | beta | 1.000576 | 1.001801 | 0.0375407 | 0.0375624 | 0.0378417 | 14253.2 | 0.0000262 | 0.95 | 0.0314411 | 0.0437422 |
| X1770 | M | 1.000298 | 1.000964 | 49.8528284 | 50.0817560 | 50.3580496 | 13551.1 | 0.0264695 | 0.95 | 43.7540998 | 55.7240017 |
| X1770 | rate | 1.000094 | 1.000275 | 0.0053016 | 0.0052956 | 0.0052041 | 27499.5 | 0.0000151 | 0.95 | 0.0004322 | 0.0101881 |
| X1780 | alpha | 1.001089 | 1.003872 | 0.0100912 | 0.0100242 | 0.0098793 | 13153.1 | 0.0000107 | 0.95 | 0.0077807 | 0.0125681 |
| X1780 | beta | 1.000765 | 1.002770 | 0.0407636 | 0.0407668 | 0.0406275 | 14796.3 | 0.0000251 | 0.95 | 0.0347108 | 0.0466753 |
| X1780 | M | 1.001100 | 1.003857 | 54.2249121 | 54.3794171 | 54.9416590 | 14389.5 | 0.0204589 | 0.95 | 49.2715760 | 58.8762349 |
| X1780 | rate | 1.000574 | 1.002146 | 0.0098681 | 0.0098605 | 0.0099363 | 27001.6 | 0.0000152 | 0.95 | 0.0049838 | 0.0147621 |
| X1790 | alpha | 1.001213 | 1.004101 | 0.0075877 | 0.0075309 | 0.0073853 | 13394.6 | 0.0000085 | 0.95 | 0.0057156 | 0.0095457 |
| X1790 | beta | 1.000912 | 1.003290 | 0.0458236 | 0.0458462 | 0.0458421 | 14781.8 | 0.0000260 | 0.95 | 0.0396890 | 0.0520899 |
| X1790 | M | 1.001011 | 1.003327 | 59.2913458 | 59.3690803 | 59.3913393 | 16477.9 | 0.0152745 | 0.95 | 55.4175368 | 63.1058941 |
| X1790 | rate | 1.000444 | 1.001551 | 0.0163690 | 0.0163788 | 0.0165687 | 24985.7 | 0.0000158 | 0.95 | 0.0115298 | 0.0213122 |
| X1800 | alpha | 1.000387 | 1.001251 | 0.0067681 | 0.0067205 | 0.0066553 | 12952.0 | 0.0000077 | 0.95 | 0.0050763 | 0.0085024 |
| X1800 | beta | 1.000332 | 1.001184 | 0.0477523 | 0.0477522 | 0.0478150 | 14065.9 | 0.0000260 | 0.95 | 0.0416756 | 0.0537888 |
| X1800 | M | 1.000285 | 1.000812 | 60.9817744 | 61.0368872 | 61.0870784 | 17235.5 | 0.0136042 | 0.95 | 57.4198438 | 64.4259602 |
| X1800 | rate | 1.000109 | 1.000405 | 0.0172752 | 0.0172792 | 0.0173804 | 24208.7 | 0.0000160 | 0.95 | 0.0123856 | 0.0221662 |
| X1810 | alpha | 1.000202 | 1.000668 | 0.0062540 | 0.0062051 | 0.0060517 | 12219.0 | 0.0000076 | 0.95 | 0.0046618 | 0.0079061 |
| X1810 | beta | 1.000300 | 1.000974 | 0.0466685 | 0.0466843 | 0.0466222 | 13819.9 | 0.0000264 | 0.95 | 0.0405736 | 0.0527045 |
| X1810 | M | 1.000099 | 1.000312 | 63.1437477 | 63.1965586 | 63.1840070 | 16815.0 | 0.0141963 | 0.95 | 59.5131108 | 66.7201334 |
| X1810 | rate | 1.000063 | 1.000170 | 0.0186911 | 0.0186887 | 0.0186977 | 21565.1 | 0.0000171 | 0.95 | 0.0138016 | 0.0236117 |
| X1820 | alpha | 1.000215 | 1.000279 | 0.0057095 | 0.0056649 | 0.0055172 | 11737.7 | 0.0000072 | 0.95 | 0.0042407 | 0.0072573 |
| X1820 | beta | 1.000270 | 1.000463 | 0.0488446 | 0.0488583 | 0.0489581 | 12730.0 | 0.0000279 | 0.95 | 0.0425629 | 0.0548806 |
| X1820 | M | 1.000058 | 1.000058 | 64.0351053 | 64.0783090 | 64.1736064 | 17185.5 | 0.0129582 | 0.95 | 60.6476942 | 67.3084873 |
| X1820 | rate | 1.000055 | 1.000145 | 0.0183072 | 0.0183033 | 0.0183194 | 21399.3 | 0.0000171 | 0.95 | 0.0134475 | 0.0232238 |
| X1830 | alpha | 1.000851 | 1.002718 | 0.0056217 | 0.0055807 | 0.0055025 | 11196.7 | 0.0000071 | 0.95 | 0.0041951 | 0.0071180 |
| X1830 | beta | 1.000811 | 1.002726 | 0.0500179 | 0.0500137 | 0.0501418 | 12016.8 | 0.0000281 | 0.95 | 0.0440217 | 0.0561384 |
| X1830 | M | 1.000547 | 1.001650 | 63.7874764 | 63.8285439 | 63.9588124 | 16675.9 | 0.0124725 | 0.95 | 60.5930623 | 66.9110171 |
| X1830 | rate | 1.000415 | 1.001353 | 0.0169139 | 0.0169158 | 0.0170653 | 21735.5 | 0.0000169 | 0.95 | 0.0119901 | 0.0217235 |
| X1840 | alpha | 1.001912 | 1.006772 | 0.0055618 | 0.0055194 | 0.0053917 | 11400.5 | 0.0000071 | 0.95 | 0.0040979 | 0.0070495 |
| X1840 | beta | 1.001683 | 1.006126 | 0.0496698 | 0.0496734 | 0.0495466 | 12494.4 | 0.0000281 | 0.95 | 0.0435270 | 0.0558486 |
| X1840 | M | 1.001165 | 1.004232 | 64.1728612 | 64.2122002 | 64.4409872 | 16778.0 | 0.0127460 | 0.95 | 60.9228836 | 67.4118054 |
| X1840 | rate | 1.000770 | 1.002796 | 0.0184375 | 0.0184351 | 0.0184647 | 20471.4 | 0.0000175 | 0.95 | 0.0135561 | 0.0233655 |
kable(London_1841_result,
caption = "Census data for London from 1841.") %>%
kableExtra::kable_styling(latex_options = c("HOLD_position","scale_down"))
| PSRF Point est. | PSRF Upper C.I. | Mean | Median | Mode | ESS | MCSE | HDImass | HDIlow | HDIhigh | |
|---|---|---|---|---|---|---|---|---|---|---|
| a | 1.000227 | 1.000481 | 0.0045780 | 0.0045654 | 0.0045126 | 15366.4 | 0.0000030 | 0.95 | 0.0038745 | 0.0053284 |
| b | 1.000173 | 1.000361 | 0.0547652 | 0.0547581 | 0.0546507 | 15261.7 | 0.0000155 | 0.95 | 0.0510256 | 0.0585294 |
| M | 1.000098 | 1.000288 | 60.3512664 | 60.3640713 | 60.4164328 | 26323.3 | 0.0044223 | 0.95 | 58.9378882 | 61.7484732 |
kable(eng_mort_result, caption = "English mortality data.") %>%
kableExtra::kable_styling(latex_options = c("HOLD_position","scale_down"))
| year | parameter | PSRF Point est. | PSRF Upper C.I. | Mean | Median | Mode | ESS | MCSE | HDImass | HDIlow | HDIhigh |
|---|---|---|---|---|---|---|---|---|---|---|---|
| X1640 | alpha | 1.000116 | 1.000213 | 0.0109640 | 0.0109440 | 0.0108724 | 20086.8 | 0.0000055 | 0.95 | 0.0094508 | 0.0125183 |
| X1640 | beta | 1.000128 | 1.000269 | 0.0473794 | 0.0473646 | 0.0471615 | 19457.0 | 0.0000160 | 0.95 | 0.0430271 | 0.0517521 |
| X1640 | M | 1.000098 | 1.000168 | 55.8790864 | 55.9257645 | 56.0762781 | 22766.9 | 0.0074788 | 0.95 | 53.6542245 | 58.0607633 |
| X1650 | alpha | 1.000196 | 1.000699 | 0.0086495 | 0.0086305 | 0.0086386 | 17477.0 | 0.0000050 | 0.95 | 0.0073694 | 0.0099516 |
| X1650 | beta | 1.000238 | 1.000818 | 0.0534298 | 0.0534191 | 0.0532174 | 17097.8 | 0.0000176 | 0.95 | 0.0488730 | 0.0579356 |
| X1650 | M | 1.000122 | 1.000456 | 59.0892102 | 59.1180884 | 59.1222939 | 22875.6 | 0.0058105 | 0.95 | 57.3707403 | 60.8059797 |
| X1660 | alpha | 1.000538 | 1.001899 | 0.0091323 | 0.0091133 | 0.0090836 | 17736.5 | 0.0000051 | 0.95 | 0.0078190 | 0.0104985 |
| X1660 | beta | 1.000442 | 1.001588 | 0.0507107 | 0.0507012 | 0.0506517 | 17263.0 | 0.0000172 | 0.95 | 0.0463039 | 0.0551739 |
| X1660 | M | 1.000484 | 1.001711 | 58.8100849 | 58.8427992 | 58.8427140 | 22595.3 | 0.0063824 | 0.95 | 56.9061034 | 60.6611103 |
| X1670 | alpha | 1.000280 | 1.000678 | 0.0109726 | 0.0109471 | 0.0109033 | 20090.3 | 0.0000056 | 0.95 | 0.0094600 | 0.0125515 |
| X1670 | beta | 1.000338 | 1.000812 | 0.0444972 | 0.0445019 | 0.0446316 | 19399.7 | 0.0000157 | 0.95 | 0.0402542 | 0.0488448 |
| X1670 | M | 1.000211 | 1.000529 | 56.4443366 | 56.5061422 | 56.5992418 | 22544.4 | 0.0083487 | 0.95 | 53.9239107 | 58.8183187 |
| X1680 | alpha | 1.000560 | 1.001531 | 0.0134499 | 0.0134251 | 0.0133309 | 22339.5 | 0.0000061 | 0.95 | 0.0116869 | 0.0152420 |
| X1680 | beta | 1.000479 | 1.001399 | 0.0435646 | 0.0435605 | 0.0437501 | 21337.1 | 0.0000151 | 0.95 | 0.0392159 | 0.0478531 |
| X1680 | M | 1.000597 | 1.001611 | 51.9412993 | 52.0117614 | 52.1884363 | 23152.8 | 0.0091727 | 0.95 | 49.1667363 | 54.6014009 |
| X1690 | alpha | 1.000203 | 1.000424 | 0.0100036 | 0.0099815 | 0.0099278 | 19068.4 | 0.0000053 | 0.95 | 0.0085828 | 0.0114492 |
| X1690 | beta | 1.000217 | 1.000487 | 0.0457255 | 0.0457144 | 0.0457837 | 18458.1 | 0.0000160 | 0.95 | 0.0414631 | 0.0499716 |
| X1690 | M | 1.000156 | 1.000323 | 58.2265512 | 58.2748183 | 58.3311613 | 22552.3 | 0.0076819 | 0.95 | 55.9044003 | 60.4191960 |
| X1700 | alpha | 1.000247 | 1.000813 | 0.0097904 | 0.0097696 | 0.0097670 | 19048.9 | 0.0000052 | 0.95 | 0.0083976 | 0.0112137 |
| X1700 | beta | 1.000228 | 1.000792 | 0.0469162 | 0.0469091 | 0.0468449 | 18524.9 | 0.0000160 | 0.95 | 0.0426635 | 0.0512282 |
| X1700 | M | 1.000210 | 1.000697 | 58.3940436 | 58.4388608 | 58.4010030 | 22362.5 | 0.0073779 | 0.95 | 56.2165699 | 60.5292073 |
| X1710 | alpha | 1.000629 | 1.002202 | 0.0076344 | 0.0076175 | 0.0075883 | 16583.9 | 0.0000046 | 0.95 | 0.0064833 | 0.0088178 |
| X1710 | beta | 1.000810 | 1.002798 | 0.0547320 | 0.0547184 | 0.0547561 | 16149.3 | 0.0000181 | 0.95 | 0.0502213 | 0.0592441 |
| X1710 | M | 1.000354 | 1.001230 | 61.0059909 | 61.0278089 | 61.0396872 | 23904.2 | 0.0053119 | 0.95 | 59.3643989 | 62.5807876 |
| X1720 | alpha | 1.000438 | 1.001584 | 0.0080028 | 0.0079824 | 0.0079301 | 17173.5 | 0.0000047 | 0.95 | 0.0068173 | 0.0092105 |
| X1720 | beta | 1.000453 | 1.001645 | 0.0560063 | 0.0560001 | 0.0558861 | 16622.0 | 0.0000179 | 0.95 | 0.0514205 | 0.0604697 |
| X1720 | M | 1.000297 | 1.001094 | 59.7548666 | 59.7785061 | 59.8227855 | 23615.5 | 0.0051845 | 0.95 | 58.1648789 | 61.2877274 |
| X1730 | alpha | 1.000128 | 1.000485 | 0.0067962 | 0.0067781 | 0.0067500 | 15125.2 | 0.0000045 | 0.95 | 0.0057413 | 0.0078882 |
| X1730 | beta | 1.000132 | 1.000481 | 0.0561362 | 0.0561233 | 0.0561525 | 14537.5 | 0.0000193 | 0.95 | 0.0516431 | 0.0607418 |
| X1730 | M | 1.000086 | 1.000325 | 62.6345173 | 62.6558894 | 62.6742840 | 23395.6 | 0.0050475 | 0.95 | 61.1122439 | 64.1406077 |
| X1740 | alpha | 1.000185 | 1.000678 | 0.0067863 | 0.0067674 | 0.0067507 | 15383.6 | 0.0000045 | 0.95 | 0.0057019 | 0.0078702 |
| X1740 | beta | 1.000260 | 1.000953 | 0.0566936 | 0.0566911 | 0.0568096 | 15043.4 | 0.0000191 | 0.95 | 0.0520709 | 0.0612724 |
| X1740 | M | 1.000063 | 1.000245 | 62.4655115 | 62.4849711 | 62.4345863 | 22893.7 | 0.0051037 | 0.95 | 60.9419302 | 63.9688404 |
| X1750 | alpha | 1.000389 | 1.001407 | 0.0053793 | 0.0053645 | 0.0053635 | 13451.8 | 0.0000040 | 0.95 | 0.0044682 | 0.0062959 |
| X1750 | beta | 1.000443 | 1.001627 | 0.0595510 | 0.0595305 | 0.0594825 | 12966.5 | 0.0000210 | 0.95 | 0.0548610 | 0.0642515 |
| X1750 | M | 1.000167 | 1.000607 | 65.4071998 | 65.4213962 | 65.4642394 | 24607.7 | 0.0044311 | 0.95 | 64.0354191 | 66.7582250 |
| X1760 | alpha | 1.000180 | 1.000387 | 0.0080565 | 0.0080378 | 0.0079359 | 17802.8 | 0.0000047 | 0.95 | 0.0068516 | 0.0092887 |
| X1760 | beta | 1.000187 | 1.000346 | 0.0488550 | 0.0488417 | 0.0488743 | 16840.4 | 0.0000169 | 0.95 | 0.0445037 | 0.0531121 |
| X1760 | M | 1.000119 | 1.000328 | 61.9016665 | 61.9336352 | 62.0050035 | 23618.5 | 0.0063598 | 0.95 | 59.9327761 | 63.7618010 |
| X1770 | alpha | 1.000469 | 1.001234 | 0.0067654 | 0.0067476 | 0.0066997 | 14881.8 | 0.0000045 | 0.95 | 0.0057073 | 0.0078687 |
| X1770 | beta | 1.000501 | 1.001341 | 0.0538935 | 0.0538804 | 0.0536262 | 14373.8 | 0.0000192 | 0.95 | 0.0494452 | 0.0584665 |
| X1770 | M | 1.000270 | 1.000709 | 63.5277738 | 63.5489910 | 63.4921572 | 22585.6 | 0.0054864 | 0.95 | 61.9173469 | 65.1383522 |
| X1780 | alpha | 1.000347 | 1.001235 | 0.0066384 | 0.0066225 | 0.0066110 | 15713.1 | 0.0000043 | 0.95 | 0.0055976 | 0.0076907 |
| X1780 | beta | 1.000349 | 1.001303 | 0.0570824 | 0.0570677 | 0.0571475 | 15127.7 | 0.0000188 | 0.95 | 0.0526292 | 0.0616896 |
| X1780 | M | 1.000195 | 1.000710 | 62.7166530 | 62.7352113 | 62.7235429 | 24154.0 | 0.0048243 | 0.95 | 61.2201635 | 64.1540268 |
| X1790 | alpha | 1.000180 | 1.000376 | 0.0058127 | 0.0057951 | 0.0057825 | 13899.0 | 0.0000042 | 0.95 | 0.0048677 | 0.0068164 |
| X1790 | beta | 1.000229 | 1.000478 | 0.0580897 | 0.0580826 | 0.0579337 | 13447.1 | 0.0000206 | 0.95 | 0.0533856 | 0.0627649 |
| X1790 | M | 1.000055 | 1.000174 | 64.6577738 | 64.6756380 | 64.7246120 | 23430.8 | 0.0047208 | 0.95 | 63.2361972 | 66.0657933 |
| X1800 | alpha | 1.000697 | 1.002167 | 0.0046142 | 0.0045977 | 0.0045567 | 12391.5 | 0.0000037 | 0.95 | 0.0038253 | 0.0054317 |
| X1800 | beta | 1.000709 | 1.002222 | 0.0608363 | 0.0608357 | 0.0608310 | 11940.3 | 0.0000219 | 0.95 | 0.0561091 | 0.0654678 |
| X1800 | M | 1.000239 | 1.000822 | 67.4325112 | 67.4451148 | 67.4486965 | 26907.8 | 0.0039816 | 0.95 | 66.1359322 | 68.6958522 |
kable(HMD_UK_result, caption = "Human Mortality Database UK.") %>%
kableExtra::kable_styling(latex_options = c("HOLD_position","scale_down"))
| year | parameter | PSRF Point est. | PSRF Upper C.I. | Mean | Median | Mode | ESS | MCSE | HDImass | HDIlow | HDIhigh |
|---|---|---|---|---|---|---|---|---|---|---|---|
| X1841 | alpha | 1.000163 | 1.000417 | 0.0036316 | 0.0036148 | 0.0035704 | 13786.9 | 0.0000032 | 0.95 | 0.0029186 | 0.0043694 |
| X1841 | beta | 1.000156 | 1.000468 | 0.0519888 | 0.0519880 | 0.0522191 | 13557.1 | 0.0000185 | 0.95 | 0.0476828 | 0.0561015 |
| X1841 | M | 1.000083 | 1.000148 | 66.2542881 | 66.2748935 | 66.3111134 | 25227.7 | 0.0056085 | 0.95 | 64.4997322 | 67.9878895 |
| X1845 | alpha | 1.000079 | 1.000297 | 0.0042938 | 0.0042780 | 0.0042669 | 14758.1 | 0.0000036 | 0.95 | 0.0034647 | 0.0051540 |
| X1845 | beta | 1.000067 | 1.000247 | 0.0498996 | 0.0498859 | 0.0500069 | 14606.7 | 0.0000180 | 0.95 | 0.0455985 | 0.0541474 |
| X1845 | M | 1.000065 | 1.000255 | 64.2120906 | 64.2353737 | 64.2258466 | 24443.1 | 0.0062539 | 0.95 | 62.2412879 | 66.0782225 |
| X1850 | alpha | 1.000973 | 1.003549 | 0.0037558 | 0.0037391 | 0.0036783 | 13963.2 | 0.0000033 | 0.95 | 0.0030110 | 0.0045196 |
| X1850 | beta | 1.000868 | 1.003159 | 0.0517607 | 0.0517548 | 0.0515669 | 13902.2 | 0.0000185 | 0.95 | 0.0475374 | 0.0561228 |
| X1850 | M | 1.000670 | 1.002447 | 65.7445767 | 65.7656894 | 65.8470383 | 24788.4 | 0.0057544 | 0.95 | 63.9683713 | 67.5152044 |
| X1855 | alpha | 1.000156 | 1.000325 | 0.0034310 | 0.0034165 | 0.0034148 | 13071.2 | 0.0000031 | 0.95 | 0.0027387 | 0.0041407 |
| X1855 | beta | 1.000111 | 1.000252 | 0.0533405 | 0.0533264 | 0.0532089 | 12901.9 | 0.0000193 | 0.95 | 0.0489858 | 0.0575821 |
| X1855 | M | 1.000055 | 1.000176 | 66.5070750 | 66.5214941 | 66.5377049 | 24496.9 | 0.0055156 | 0.95 | 64.7810996 | 68.1628553 |
| X1860 | alpha | 1.000103 | 1.000169 | 0.0034785 | 0.0034615 | 0.0034062 | 13432.3 | 0.0000031 | 0.95 | 0.0027794 | 0.0041924 |
| X1860 | beta | 1.000118 | 1.000200 | 0.0532621 | 0.0532640 | 0.0532106 | 13350.6 | 0.0000189 | 0.95 | 0.0490210 | 0.0575846 |
| X1860 | M | 1.000016 | 1.000032 | 66.2956647 | 66.3134949 | 66.3500169 | 24949.1 | 0.0054798 | 0.95 | 64.5756127 | 67.9675086 |
| X1865 | alpha | 1.000093 | 1.000333 | 0.0035991 | 0.0035837 | 0.0035330 | 13810.1 | 0.0000031 | 0.95 | 0.0028932 | 0.0043267 |
| X1865 | beta | 1.000108 | 1.000353 | 0.0530530 | 0.0530491 | 0.0530859 | 13658.1 | 0.0000185 | 0.95 | 0.0488013 | 0.0572954 |
| X1865 | M | 1.000045 | 1.000177 | 65.7780212 | 65.7953467 | 65.8802464 | 25507.4 | 0.0054316 | 0.95 | 64.0717897 | 67.4665740 |
| X1870 | alpha | 1.000077 | 1.000191 | 0.0035027 | 0.0034908 | 0.0034765 | 13760.3 | 0.0000030 | 0.95 | 0.0028292 | 0.0042127 |
| X1870 | beta | 1.000110 | 1.000242 | 0.0536849 | 0.0536587 | 0.0535650 | 13616.9 | 0.0000184 | 0.95 | 0.0495385 | 0.0579499 |
| X1870 | M | 1.000013 | 1.000070 | 65.9071237 | 65.9205478 | 65.8577523 | 25746.8 | 0.0052524 | 0.95 | 64.2645935 | 67.5678728 |
| X1875 | alpha | 1.000092 | 1.000343 | 0.0030605 | 0.0030478 | 0.0030211 | 12815.0 | 0.0000028 | 0.95 | 0.0024475 | 0.0036823 |
| X1875 | beta | 1.000131 | 1.000471 | 0.0568401 | 0.0568279 | 0.0568980 | 12685.7 | 0.0000193 | 0.95 | 0.0526071 | 0.0611415 |
| X1875 | M | 1.000031 | 1.000141 | 66.4668857 | 66.4785272 | 66.5086127 | 26537.0 | 0.0047162 | 0.95 | 64.9506366 | 67.9602202 |
| X1880 | alpha | 1.000119 | 1.000291 | 0.0027376 | 0.0027242 | 0.0026867 | 12292.1 | 0.0000026 | 0.95 | 0.0021904 | 0.0033047 |
| X1880 | beta | 1.000171 | 1.000388 | 0.0580794 | 0.0580802 | 0.0580583 | 12275.9 | 0.0000195 | 0.95 | 0.0538930 | 0.0623071 |
| X1880 | M | 1.000016 | 1.000046 | 67.6639684 | 67.6752899 | 67.6594434 | 26763.5 | 0.0045057 | 0.95 | 66.2138218 | 69.0997903 |
| X1885 | alpha | 1.000329 | 1.000699 | 0.0024297 | 0.0024169 | 0.0023954 | 11472.9 | 0.0000024 | 0.95 | 0.0019319 | 0.0029532 |
| X1885 | beta | 1.000279 | 1.000617 | 0.0605593 | 0.0605577 | 0.0605172 | 11375.3 | 0.0000207 | 0.95 | 0.0561612 | 0.0648427 |
| X1885 | M | 1.000124 | 1.000309 | 68.1749533 | 68.1842585 | 68.1928238 | 26834.9 | 0.0042250 | 0.95 | 66.8018933 | 69.5153058 |
| X1890 | alpha | 1.000121 | 1.000451 | 0.0024118 | 0.0023997 | 0.0023802 | 11867.7 | 0.0000024 | 0.95 | 0.0019247 | 0.0029285 |
| X1890 | beta | 1.000146 | 1.000531 | 0.0614665 | 0.0614588 | 0.0613662 | 11669.1 | 0.0000205 | 0.95 | 0.0571518 | 0.0657954 |
| X1890 | M | 1.000045 | 1.000148 | 67.7519542 | 67.7613179 | 67.8037905 | 28081.6 | 0.0040695 | 0.95 | 66.4069818 | 69.0759956 |
| X1895 | alpha | 1.000328 | 1.001210 | 0.0019825 | 0.0019735 | 0.0019634 | 10586.6 | 0.0000021 | 0.95 | 0.0015598 | 0.0024219 |
| X1895 | beta | 1.000267 | 1.000994 | 0.0637922 | 0.0637712 | 0.0636859 | 10594.5 | 0.0000217 | 0.95 | 0.0594245 | 0.0681856 |
| X1895 | M | 1.000224 | 1.000819 | 69.4924393 | 69.4994274 | 69.5249671 | 28489.7 | 0.0038280 | 0.95 | 68.2103261 | 70.7410684 |
| X1900 | alpha | 1.000051 | 1.000194 | 0.0017882 | 0.0017794 | 0.0017686 | 10113.1 | 0.0000020 | 0.95 | 0.0013975 | 0.0021792 |
| X1900 | beta | 1.000061 | 1.000247 | 0.0653147 | 0.0653019 | 0.0653664 | 10036.7 | 0.0000222 | 0.95 | 0.0609626 | 0.0696771 |
| X1900 | M | 1.000007 | 1.000020 | 70.1656919 | 70.1713832 | 70.1615274 | 28126.0 | 0.0036879 | 0.95 | 68.9548389 | 71.3801825 |
kable(peers_result, caption = "English Peers.") %>%
kableExtra::kable_styling(latex_options = c("HOLD_position","scale_down"))
| PSRF Point est. | PSRF Upper C.I. | Mean | Median | Mode | ESS | MCSE | HDImass | HDIlow | HDIhigh | |
|---|---|---|---|---|---|---|---|---|---|---|
| a | 1.000356 | 1.001061 | 0.0044095 | 0.0043879 | 0.0043263 | 11315.3 | 0.0000044 | 0.95 | 0.0035238 | 0.0053575 |
| b | 1.000307 | 1.000854 | 0.0609452 | 0.0609518 | 0.0612976 | 11121.9 | 0.0000244 | 0.95 | 0.0559415 | 0.0660412 |
| M | 1.000196 | 1.000696 | 58.1500750 | 58.1648975 | 58.1757927 | 20660.4 | 0.0059675 | 0.95 | 56.4492001 | 59.8036275 |
kable(monks_result, caption = "Christ Church monks.") %>%
kableExtra::kable_styling(latex_options = c("HOLD_position","scale_down"))
| start | end | parameter | PSRF Point est. | PSRF Upper C.I. | Mean | Median | Mode | ESS | MCSE | HDImass | HDIlow | HDIhigh |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1395 | 1505 | alpha | 1.000569 | 1.001661 | 0.0102993 | 0.0102563 | 0.0100488 | 13991.9 | 0.0000096 | 0.95 | 0.0081076 | 0.0125497 |
| 1395 | 1505 | beta | 1.000498 | 1.001436 | 0.0459467 | 0.0459287 | 0.0461060 | 13623.6 | 0.0000273 | 0.95 | 0.0397953 | 0.0523389 |
| 1395 | 1505 | M | 1.000504 | 1.001504 | 52.5281106 | 52.6296486 | 52.7658924 | 15808.5 | 0.0143226 | 0.95 | 48.9344189 | 55.9631681 |
The data is mainly hard coded in the file ./chapter_04_results/Wellcome_DB.R.
Only St. Bride’s crypt is excluded but available from the Museum of London upon request. For general information: https://www.museumoflondon.org.uk go for: Collections > Archaeology at the Museum of London > Wellcome Osteological Research Database > St. Bride’s Church Fleet Street. If runCodeNew == TRUE the file ./lifetables_processing/stbrides_crypt.R will ask for the location of the retrieved dataset (Excel sheet) and process the data. In any other case pre-processed data will be loaded.
source("./lifetables_processing/stbrides_crypt.R")
source("./chapter_04_results/Wellcome_DB.R")
kable(wellcome_result) %>%
kableExtra::kable_styling(latex_options = c("HOLD_position","scale_down"))
| cemetery | start | end | parameter | PSRF Point est. | PSRF Upper C.I. | Mean | Median | Mode | ESS | MCSE | HDImass | HDIlow | HDIhigh |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Bermondsey Abbey | 1089 | 1538 | alpha | 1.000095 | 1.000352 | 0.0119872 | 0.0118695 | 0.0117349 | 26882.4 | 0.0000115 | 0.95 | 0.0084108 | 0.0157410 |
| Bermondsey Abbey | 1089 | 1538 | beta | 1.000115 | 1.000319 | 0.0410531 | 0.0410516 | 0.0413654 | 23098.5 | 0.0000312 | 0.95 | 0.0318561 | 0.0503895 |
| Bermondsey Abbey | 1089 | 1538 | M | 1.000071 | 1.000266 | 41.8366810 | 42.1437778 | 42.5664355 | 29309.6 | 0.0207896 | 0.95 | 34.6719658 | 48.4310632 |
| St. Mary Graces | 1350 | 1540 | alpha | 1.000196 | 1.000732 | 0.0197808 | 0.0196850 | 0.0195223 | 35662.0 | 0.0000118 | 0.95 | 0.0154857 | 0.0241619 |
| St. Mary Graces | 1350 | 1540 | beta | 1.000244 | 1.000894 | 0.0346722 | 0.0346636 | 0.0349129 | 29450.8 | 0.0000239 | 0.95 | 0.0266567 | 0.0427213 |
| St. Mary Graces | 1350 | 1540 | M | 1.000288 | 1.000951 | 27.6620555 | 28.2853721 | 29.0829030 | 31343.0 | 0.0275212 | 0.95 | 17.7908628 | 36.1544161 |
| St. Mary Hospital, 1120-1200 | 1120 | 1200 | alpha | 1.000021 | 1.000058 | 0.0249328 | 0.0248411 | 0.0247596 | 47240.6 | 0.0000108 | 0.95 | 0.0203838 | 0.0295337 |
| St. Mary Hospital, 1120-1200 | 1120 | 1200 | beta | 1.000010 | 1.000041 | 0.0363031 | 0.0363142 | 0.0366087 | 42155.0 | 0.0000184 | 0.95 | 0.0288655 | 0.0437148 |
| St. Mary Hospital, 1120-1200 | 1120 | 1200 | M | 1.000014 | 1.000048 | 21.9000883 | 22.4278307 | 23.6171674 | 41316.5 | 0.0217592 | 0.95 | 12.9358328 | 29.6933479 |
| St. Mary Hospital, 1200-1250 | 1200 | 1250 | alpha | 1.000142 | 1.000479 | 0.0299501 | 0.0298832 | 0.0296347 | 50227.8 | 0.0000103 | 0.95 | 0.0254561 | 0.0345077 |
| St. Mary Hospital, 1200-1250 | 1200 | 1250 | beta | 1.000145 | 1.000390 | 0.0356927 | 0.0356959 | 0.0355017 | 44544.0 | 0.0000163 | 0.95 | 0.0288836 | 0.0423855 |
| St. Mary Hospital, 1200-1250 | 1200 | 1250 | M | 1.000138 | 1.000388 | 16.4726206 | 16.9685941 | 17.8228768 | 43773.7 | 0.0209091 | 0.95 | 7.6941741 | 24.3391668 |
| St. Mary Hospital, 1250-1400 | 1250 | 1400 | alpha | 1.000058 | 1.000230 | 0.0183232 | 0.0182986 | 0.0182568 | 30711.1 | 0.0000060 | 0.95 | 0.0162397 | 0.0203837 |
| St. Mary Hospital, 1250-1400 | 1250 | 1400 | beta | 1.000039 | 1.000160 | 0.0580756 | 0.0580643 | 0.0577145 | 27569.9 | 0.0000162 | 0.95 | 0.0529190 | 0.0634424 |
| St. Mary Hospital, 1250-1400 | 1250 | 1400 | M | 1.000056 | 1.000226 | 31.8403051 | 31.8802975 | 31.9815271 | 32452.4 | 0.0050096 | 0.95 | 30.0460798 | 33.5688087 |
| St. Mary Hospital, 1400-1539 | 1400 | 1539 | alpha | 1.000184 | 1.000413 | 0.0262455 | 0.0261845 | 0.0258468 | 45106.6 | 0.0000098 | 0.95 | 0.0222297 | 0.0303974 |
| St. Mary Hospital, 1400-1539 | 1400 | 1539 | beta | 1.000202 | 1.000384 | 0.0374668 | 0.0374646 | 0.0373648 | 37992.2 | 0.0000178 | 0.95 | 0.0307176 | 0.0443176 |
| St. Mary Hospital, 1400-1539 | 1400 | 1539 | M | 1.000255 | 1.000509 | 21.1562579 | 21.5422484 | 22.2118499 | 38394.6 | 0.0188420 | 0.95 | 13.7317283 | 27.8355824 |
| New Churchyard | 1569 | 1739 | alpha | 1.000100 | 1.000375 | 0.0257447 | 0.0256826 | 0.0256229 | 40693.9 | 0.0000097 | 0.95 | 0.0219664 | 0.0296497 |
| New Churchyard | 1569 | 1739 | beta | 1.000143 | 1.000447 | 0.0365472 | 0.0365523 | 0.0364771 | 33659.4 | 0.0000185 | 0.95 | 0.0298776 | 0.0431955 |
| New Churchyard | 1569 | 1739 | M | 1.000167 | 1.000489 | 21.2258180 | 21.6422371 | 22.4873708 | 34065.6 | 0.0202506 | 0.95 | 13.6829257 | 27.9012158 |
| St. Benet Sherehog | 1670 | 1740 | alpha | 1.000103 | 1.000388 | 0.0159324 | 0.0158024 | 0.0157241 | 35332.7 | 0.0000126 | 0.95 | 0.0114989 | 0.0206750 |
| St. Benet Sherehog | 1670 | 1740 | beta | 1.000166 | 1.000541 | 0.0354819 | 0.0354675 | 0.0352938 | 29914.9 | 0.0000268 | 0.95 | 0.0265131 | 0.0446216 |
| St. Benet Sherehog | 1670 | 1740 | M | 1.000123 | 1.000414 | 34.0694974 | 34.7174821 | 36.0672253 | 33191.8 | 0.0286473 | 0.95 | 23.6417236 | 43.3454393 |
| Chelsea Old church | 1712 | 1842 | alpha | 1.000092 | 1.000284 | 0.0083989 | 0.0083033 | 0.0082201 | 24055.1 | 0.0000095 | 0.95 | 0.0056545 | 0.0113658 |
| Chelsea Old church | 1712 | 1842 | beta | 1.000107 | 1.000363 | 0.0422444 | 0.0421520 | 0.0421527 | 20068.2 | 0.0000343 | 0.95 | 0.0327982 | 0.0517568 |
| Chelsea Old church | 1712 | 1842 | M | 1.000066 | 1.000214 | 50.2412943 | 50.4255236 | 50.6944550 | 32126.8 | 0.0173728 | 0.95 | 43.9580757 | 56.1242381 |
| St. Marylebone | 1742 | 1817 | alpha | 1.000026 | 1.000095 | 0.0125953 | 0.0125006 | 0.0123046 | 29334.6 | 0.0000102 | 0.95 | 0.0092608 | 0.0160318 |
| St. Marylebone | 1742 | 1817 | beta | 1.000017 | 1.000034 | 0.0420937 | 0.0420895 | 0.0423370 | 23957.1 | 0.0000291 | 0.95 | 0.0331445 | 0.0508272 |
| St. Marylebone | 1742 | 1817 | M | 1.000036 | 1.000085 | 40.5179648 | 40.7766676 | 41.3760128 | 31991.5 | 0.0170220 | 0.95 | 34.3796076 | 46.1332104 |
| St. Marylebone Paddington Street north | 1772 | 1853 | alpha | 1.000045 | 1.000166 | 0.0099037 | 0.0098127 | 0.0096774 | 27403.8 | 0.0000087 | 0.95 | 0.0071709 | 0.0127837 |
| St. Marylebone Paddington Street north | 1772 | 1853 | beta | 1.000055 | 1.000206 | 0.0488613 | 0.0488575 | 0.0485839 | 23270.2 | 0.0000301 | 0.95 | 0.0398523 | 0.0578266 |
| St. Marylebone Paddington Street north | 1772 | 1853 | M | 1.000039 | 1.000116 | 44.6690555 | 44.7919466 | 45.0496301 | 37001.7 | 0.0116510 | 0.95 | 40.1953904 | 48.9817326 |
| St. Bride’s lower churchyard | 1770 | 1849 | alpha | 1.000035 | 1.000073 | 0.0061790 | 0.0061316 | 0.0059751 | 14779.1 | 0.0000071 | 0.95 | 0.0045330 | 0.0078754 |
| St. Bride’s lower churchyard | 1770 | 1849 | beta | 1.000155 | 1.000339 | 0.0510752 | 0.0510280 | 0.0511331 | 11203.6 | 0.0000422 | 0.95 | 0.0423814 | 0.0598976 |
| St. Bride’s lower churchyard | 1770 | 1849 | M | 1.000130 | 1.000460 | 53.4368072 | 53.4511152 | 53.4536777 | 46992.7 | 0.0074618 | 0.95 | 50.2090353 | 56.5697935 |
| Sheen’s burial ground | 1763 | 1854 | alpha | 1.000091 | 1.000320 | 0.0129642 | 0.0128270 | 0.0124596 | 28565.8 | 0.0000128 | 0.95 | 0.0089230 | 0.0173233 |
| Sheen’s burial ground | 1763 | 1854 | beta | 1.000171 | 1.000495 | 0.0353994 | 0.0353305 | 0.0350479 | 24673.6 | 0.0000300 | 0.95 | 0.0262620 | 0.0446735 |
| Sheen’s burial ground | 1763 | 1854 | M | 1.000120 | 1.000420 | 39.9956498 | 40.5717091 | 41.5741951 | 29050.5 | 0.0299067 | 0.95 | 29.5817256 | 49.0658033 |
| Bow Baptist Church | 1816 | 1854 | alpha | 1.000037 | 1.000121 | 0.0177742 | 0.0176655 | 0.0171967 | 37363.4 | 0.0000114 | 0.95 | 0.0135868 | 0.0221462 |
| Bow Baptist Church | 1816 | 1854 | beta | 1.000013 | 1.000063 | 0.0344658 | 0.0344556 | 0.0344680 | 30272.0 | 0.0000249 | 0.95 | 0.0259810 | 0.0429301 |
| Bow Baptist Church | 1816 | 1854 | M | 1.000031 | 1.000063 | 30.6580796 | 31.3283020 | 32.6360138 | 33171.9 | 0.0277771 | 0.95 | 20.3999444 | 39.3695617 |
| St. Mary and St. Michael | 1843 | 1853 | alpha | 1.000523 | 1.001826 | 0.0186478 | 0.0185639 | 0.0182508 | 41699.1 | 0.0000099 | 0.95 | 0.0148267 | 0.0227130 |
| St. Mary and St. Michael | 1843 | 1853 | beta | 1.000441 | 1.001467 | 0.0402140 | 0.0402172 | 0.0404972 | 35162.0 | 0.0000216 | 0.95 | 0.0322916 | 0.0481568 |
| St. Mary and St. Michael | 1843 | 1853 | M | 1.000616 | 1.001944 | 30.8426109 | 31.1889790 | 31.6656994 | 38394.2 | 0.0171194 | 0.95 | 24.1587401 | 36.9724139 |
| St. Bride’s crypt (known age) | 1740 | 1853 | alpha | 1.001301 | 1.004385 | 0.0048650 | 0.0048100 | 0.0046364 | 11054.4 | 0.0000077 | 0.95 | 0.0033513 | 0.0064885 |
| St. Bride’s crypt (known age) | 1740 | 1853 | beta | 1.001527 | 1.004999 | 0.0492998 | 0.0492831 | 0.0490777 | 10841.1 | 0.0000350 | 0.95 | 0.0422819 | 0.0564716 |
| St. Bride’s crypt (known age) | 1740 | 1853 | M | 1.000820 | 1.002819 | 59.1168993 | 59.1961001 | 59.4409448 | 16528.6 | 0.0139187 | 0.95 | 55.5069567 | 62.4858268 |
| St. Bride’s crypt (estimates) | 1740 | 1853 | alpha | 1.000667 | 1.001933 | 0.0050596 | 0.0049986 | 0.0049298 | 13764.5 | 0.0000077 | 0.95 | 0.0033634 | 0.0068603 |
| St. Bride’s crypt (estimates) | 1740 | 1853 | beta | 1.000585 | 1.001723 | 0.0462335 | 0.0461153 | 0.0454728 | 11584.8 | 0.0000403 | 0.95 | 0.0377323 | 0.0547333 |
| St. Bride’s crypt (estimates) | 1740 | 1853 | M | 1.000256 | 1.000830 | 60.0338767 | 60.0689768 | 60.0228465 | 29593.8 | 0.0137494 | 0.95 | 55.4311154 | 64.7087860 |
kable(wellcome_result_r, caption = "London cemeteries data, corrected for population growth.") %>%
kableExtra::kable_styling(latex_options = c("HOLD_position","scale_down"))
| cemetery | start | end | parameter | PSRF Point est. | PSRF Upper C.I. | Mean | Median | Mode | ESS | MCSE | HDImass | HDIlow | HDIhigh |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Bermondsey Abbey | 1089 | 1538 | alpha | 1.0004384 | 1.0015608 | 0.0100569 | 0.0099338 | 0.0097741 | 26240.3 | 0.0000109 | 0.95 | 0.0067655 | 0.0136223 |
| Bermondsey Abbey | 1089 | 1538 | beta | 1.0003921 | 1.0013937 | 0.0433703 | 0.0433773 | 0.0439068 | 23240.1 | 0.0000321 | 0.95 | 0.0336783 | 0.0528649 |
| Bermondsey Abbey | 1089 | 1538 | M | 1.0004266 | 1.0014866 | 45.6822436 | 45.8835839 | 46.3326136 | 31446.6 | 0.0191945 | 0.95 | 38.8667009 | 52.1542950 |
| Bermondsey Abbey | 1089 | 1538 | rate | 1.0000854 | 1.0002686 | 0.0056417 | 0.0056377 | 0.0056041 | 102807.2 | 0.0000078 | 0.95 | 0.0007694 | 0.0105372 |
| St. Mary Graces | 1350 | 1540 | alpha | 1.0000932 | 1.0003161 | 0.0170437 | 0.0169434 | 0.0165866 | 33968.9 | 0.0000118 | 0.95 | 0.0128337 | 0.0213373 |
| St. Mary Graces | 1350 | 1540 | beta | 1.0001339 | 1.0004049 | 0.0371500 | 0.0371640 | 0.0372066 | 29663.0 | 0.0000246 | 0.95 | 0.0288233 | 0.0454699 |
| St. Mary Graces | 1350 | 1540 | M | 1.0001704 | 1.0003953 | 32.6280813 | 33.0720564 | 34.0698466 | 31395.2 | 0.0239922 | 0.95 | 24.0736465 | 40.3502861 |
| St. Mary Graces | 1350 | 1540 | rate | 1.0000468 | 1.0001575 | 0.0050180 | 0.0050153 | 0.0049096 | 99929.5 | 0.0000079 | 0.95 | 0.0001584 | 0.0099181 |
| St. Mary Hospital, 1120-1200 | 1120 | 1200 | alpha | 1.0000497 | 1.0001475 | 0.0228863 | 0.0227945 | 0.0226674 | 43639.6 | 0.0000115 | 0.95 | 0.0183315 | 0.0276910 |
| St. Mary Hospital, 1120-1200 | 1120 | 1200 | beta | 1.0000265 | 1.0000918 | 0.0379803 | 0.0379876 | 0.0382392 | 42254.5 | 0.0000186 | 0.95 | 0.0304388 | 0.0454329 |
| St. Mary Hospital, 1120-1200 | 1120 | 1200 | M | 1.0000797 | 1.0001963 | 24.9927341 | 25.4146781 | 26.3099807 | 40134.0 | 0.0201904 | 0.95 | 16.8250371 | 32.3104430 |
| St. Mary Hospital, 1120-1200 | 1120 | 1200 | rate | 0.9999984 | 1.0000119 | 0.0028410 | 0.0028475 | 0.0030828 | 117798.6 | 0.0000072 | 0.95 | -0.0020372 | 0.0077045 |
| St. Mary Hospital, 1200-1250 | 1200 | 1250 | alpha | 1.0000343 | 1.0001359 | 0.0231140 | 0.0230386 | 0.0229749 | 51291.4 | 0.0000094 | 0.95 | 0.0190446 | 0.0273729 |
| St. Mary Hospital, 1200-1250 | 1200 | 1250 | beta | 1.0000008 | 1.0000202 | 0.0397849 | 0.0397884 | 0.0399445 | 50597.0 | 0.0000158 | 0.95 | 0.0328000 | 0.0467253 |
| St. Mary Hospital, 1200-1250 | 1200 | 1250 | M | 1.0000240 | 1.0001056 | 25.4098843 | 25.7089747 | 26.2940231 | 46409.7 | 0.0150953 | 0.95 | 18.8815567 | 31.4366781 |
| St. Mary Hospital, 1200-1250 | 1200 | 1250 | rate | 1.0000671 | 1.0002342 | 0.0127644 | 0.0127643 | 0.0128244 | 107720.3 | 0.0000076 | 0.95 | 0.0078479 | 0.0175967 |
| St. Mary Hospital, 1250-1400 | 1250 | 1400 | alpha | 1.0000605 | 1.0000968 | 0.0162303 | 0.0161956 | 0.0161827 | 23843.8 | 0.0000076 | 0.95 | 0.0139644 | 0.0185425 |
| St. Mary Hospital, 1250-1400 | 1250 | 1400 | beta | 1.0000277 | 1.0000352 | 0.0610335 | 0.0610352 | 0.0607921 | 24621.2 | 0.0000177 | 0.95 | 0.0556105 | 0.0665374 |
| St. Mary Hospital, 1250-1400 | 1250 | 1400 | M | 1.0000627 | 1.0001135 | 33.6949925 | 33.7284165 | 33.7756040 | 26097.4 | 0.0062172 | 0.95 | 31.6778781 | 35.6134228 |
| St. Mary Hospital, 1250-1400 | 1250 | 1400 | rate | 1.0000509 | 1.0000976 | 0.0048756 | 0.0048759 | 0.0049617 | 54702.2 | 0.0000105 | 0.95 | 0.0001435 | 0.0097655 |
| St. Mary Hospital, 1400-1539 | 1400 | 1539 | alpha | 1.0000461 | 1.0001787 | 0.0232316 | 0.0231524 | 0.0229215 | 42351.0 | 0.0000104 | 0.95 | 0.0191346 | 0.0274639 |
| St. Mary Hospital, 1400-1539 | 1400 | 1539 | beta | 1.0000550 | 1.0001895 | 0.0398928 | 0.0399066 | 0.0399522 | 39626.5 | 0.0000177 | 0.95 | 0.0329083 | 0.0467406 |
| St. Mary Hospital, 1400-1539 | 1400 | 1539 | M | 1.0000630 | 1.0002150 | 25.3123997 | 25.6153914 | 25.9205036 | 38299.9 | 0.0166589 | 0.95 | 18.7791532 | 31.3249516 |
| St. Mary Hospital, 1400-1539 | 1400 | 1539 | rate | 1.0000106 | 1.0000576 | 0.0047462 | 0.0047493 | 0.0047761 | 102965.2 | 0.0000077 | 0.95 | -0.0000588 | 0.0096690 |
| New Churchyard | 1569 | 1739 | alpha | 1.0000443 | 1.0000878 | 0.0214708 | 0.0214006 | 0.0209663 | 37634.3 | 0.0000101 | 0.95 | 0.0177193 | 0.0253465 |
| New Churchyard | 1569 | 1739 | beta | 1.0001137 | 1.0002395 | 0.0399080 | 0.0399144 | 0.0398191 | 34807.5 | 0.0000187 | 0.95 | 0.0330545 | 0.0467203 |
| New Churchyard | 1569 | 1739 | M | 1.0001096 | 1.0002228 | 27.3135812 | 27.5906580 | 28.2926994 | 34445.2 | 0.0165348 | 0.95 | 21.1340430 | 32.9495481 |
| New Churchyard | 1569 | 1739 | rate | 1.0000195 | 1.0000586 | 0.0075658 | 0.0075639 | 0.0075793 | 87658.4 | 0.0000084 | 0.95 | 0.0026693 | 0.0124236 |
| St. Benet Sherehog | 1670 | 1740 | alpha | 1.0001384 | 1.0005211 | 0.0135181 | 0.0133737 | 0.0130458 | 33103.2 | 0.0000123 | 0.95 | 0.0093450 | 0.0180349 |
| St. Benet Sherehog | 1670 | 1740 | beta | 1.0002094 | 1.0006563 | 0.0377790 | 0.0377933 | 0.0378383 | 29389.9 | 0.0000283 | 0.95 | 0.0282675 | 0.0472846 |
| St. Benet Sherehog | 1670 | 1740 | M | 1.0001248 | 1.0004113 | 38.9022566 | 39.3863806 | 40.2827832 | 33435.8 | 0.0255764 | 0.95 | 29.5999300 | 47.4994365 |
| St. Benet Sherehog | 1670 | 1740 | rate | 1.0000249 | 1.0001064 | 0.0054268 | 0.0054189 | 0.0052620 | 113812.2 | 0.0000074 | 0.95 | 0.0005475 | 0.0103210 |
| Chelsea Old church | 1712 | 1842 | alpha | 1.0001480 | 1.0002573 | 0.0064751 | 0.0063650 | 0.0061572 | 23987.2 | 0.0000085 | 0.95 | 0.0040732 | 0.0090999 |
| Chelsea Old church | 1712 | 1842 | beta | 1.0002599 | 1.0005036 | 0.0453886 | 0.0454175 | 0.0458495 | 19708.4 | 0.0000382 | 0.95 | 0.0347547 | 0.0557406 |
| Chelsea Old church | 1712 | 1842 | M | 1.0000299 | 1.0000809 | 55.0713758 | 55.1425610 | 55.3075641 | 43979.1 | 0.0148353 | 0.95 | 48.9491500 | 61.2053202 |
| Chelsea Old church | 1712 | 1842 | rate | 1.0000055 | 1.0000176 | 0.0075938 | 0.0075935 | 0.0077701 | 91647.9 | 0.0000082 | 0.95 | 0.0027064 | 0.0124833 |
| St. Marylebone | 1742 | 1817 | alpha | 1.0002096 | 1.0006937 | 0.0101454 | 0.0100403 | 0.0096732 | 29247.2 | 0.0000094 | 0.95 | 0.0071183 | 0.0133209 |
| St. Marylebone | 1742 | 1817 | beta | 1.0001959 | 1.0007254 | 0.0451219 | 0.0451403 | 0.0452213 | 25685.0 | 0.0000291 | 0.95 | 0.0358427 | 0.0541354 |
| St. Marylebone | 1742 | 1817 | M | 1.0001775 | 1.0005507 | 45.0630043 | 45.2182975 | 45.4917442 | 36807.9 | 0.0148453 | 0.95 | 39.3682842 | 50.5105928 |
| St. Marylebone | 1742 | 1817 | rate | 1.0000264 | 1.0001090 | 0.0074627 | 0.0074645 | 0.0074099 | 101468.4 | 0.0000078 | 0.95 | 0.0025035 | 0.0122621 |
| St. Marylebone Paddington Street north | 1772 | 1853 | alpha | 1.0000658 | 1.0001793 | 0.0067701 | 0.0066902 | 0.0064467 | 28487.4 | 0.0000068 | 0.95 | 0.0046537 | 0.0090813 |
| St. Marylebone Paddington Street north | 1772 | 1853 | beta | 1.0002920 | 1.0009451 | 0.0540540 | 0.0540386 | 0.0537952 | 25941.0 | 0.0000294 | 0.95 | 0.0447935 | 0.0633352 |
| St. Marylebone Paddington Street north | 1772 | 1853 | M | 1.0000059 | 1.0000339 | 50.5697372 | 50.5848711 | 50.6009045 | 50608.7 | 0.0096803 | 0.95 | 46.2707037 | 54.8331587 |
| St. Marylebone Paddington Street north | 1772 | 1853 | rate | 1.0000299 | 1.0001073 | 0.0134441 | 0.0134422 | 0.0134743 | 101318.9 | 0.0000078 | 0.95 | 0.0085652 | 0.0183044 |
| St. Bride’s lower churchyard | 1770 | 1849 | alpha | 1.0004322 | 1.0014789 | 0.0038814 | 0.0038350 | 0.0037138 | 15446.1 | 0.0000053 | 0.95 | 0.0026400 | 0.0051734 |
| St. Bride’s lower churchyard | 1770 | 1849 | beta | 1.0010900 | 1.0037600 | 0.0576544 | 0.0576445 | 0.0577487 | 12270.4 | 0.0000429 | 0.95 | 0.0483361 | 0.0669182 |
| St. Bride’s lower churchyard | 1770 | 1849 | M | 1.0001688 | 1.0005250 | 59.0047132 | 58.9475585 | 58.8194768 | 40939.7 | 0.0095875 | 0.95 | 55.2666792 | 62.8844643 |
| St. Bride’s lower churchyard | 1770 | 1849 | rate | 1.0000394 | 1.0001612 | 0.0132584 | 0.0132596 | 0.0130524 | 51199.2 | 0.0000110 | 0.95 | 0.0083901 | 0.0181456 |
| Sheen’s burial ground | 1763 | 1854 | alpha | 1.0000293 | 1.0000680 | 0.0084873 | 0.0083593 | 0.0081090 | 30274.8 | 0.0000097 | 0.95 | 0.0053490 | 0.0118633 |
| Sheen’s burial ground | 1763 | 1854 | beta | 1.0000180 | 1.0000412 | 0.0406644 | 0.0406625 | 0.0407175 | 27222.0 | 0.0000314 | 0.95 | 0.0305497 | 0.0508194 |
| Sheen’s burial ground | 1763 | 1854 | M | 1.0000358 | 1.0000988 | 50.5692812 | 50.7601405 | 51.1279864 | 39066.8 | 0.0202627 | 0.95 | 42.5612107 | 58.2859301 |
| Sheen’s burial ground | 1763 | 1854 | rate | 0.9999938 | 0.9999965 | 0.0131468 | 0.0131420 | 0.0130719 | 103861.1 | 0.0000077 | 0.95 | 0.0082953 | 0.0180378 |
| Bow Baptist Church | 1816 | 1854 | alpha | 1.0001794 | 1.0006411 | 0.0110382 | 0.0109321 | 0.0107885 | 42063.6 | 0.0000081 | 0.95 | 0.0078918 | 0.0143754 |
| Bow Baptist Church | 1816 | 1854 | beta | 1.0000875 | 1.0003385 | 0.0407854 | 0.0408127 | 0.0410007 | 36030.6 | 0.0000239 | 0.95 | 0.0318381 | 0.0496526 |
| Bow Baptist Church | 1816 | 1854 | M | 1.0001823 | 1.0006454 | 43.9628080 | 44.1658715 | 44.3668412 | 48157.6 | 0.0152389 | 0.95 | 37.3316415 | 50.3647476 |
| Bow Baptist Church | 1816 | 1854 | rate | 1.0000471 | 1.0001859 | 0.0174518 | 0.0174583 | 0.0173503 | 105037.5 | 0.0000077 | 0.95 | 0.0126640 | 0.0224305 |
| St. Mary and St. Michael | 1843 | 1853 | alpha | 1.0000453 | 1.0000833 | 0.0122773 | 0.0121962 | 0.0121064 | 44999.3 | 0.0000075 | 0.95 | 0.0092535 | 0.0154473 |
| St. Mary and St. Michael | 1843 | 1853 | beta | 1.0001569 | 1.0004401 | 0.0459527 | 0.0459641 | 0.0460400 | 42305.4 | 0.0000203 | 0.95 | 0.0378064 | 0.0541617 |
| St. Mary and St. Michael | 1843 | 1853 | M | 1.0000225 | 1.0000500 | 40.6854815 | 40.8011992 | 41.0795546 | 51268.0 | 0.0110280 | 0.95 | 35.7249958 | 45.4780928 |
| St. Mary and St. Michael | 1843 | 1853 | rate | 1.0000285 | 1.0000843 | 0.0176492 | 0.0176411 | 0.0176163 | 114015.4 | 0.0000074 | 0.95 | 0.0127677 | 0.0225102 |
| St. Bride’s crypt (known age) | 1740 | 1853 | alpha | 1.0004443 | 1.0013905 | 0.0032673 | 0.0032272 | 0.0031669 | 12848.3 | 0.0000049 | 0.95 | 0.0022166 | 0.0043711 |
| St. Bride’s crypt (known age) | 1740 | 1853 | beta | 1.0004021 | 1.0012201 | 0.0548600 | 0.0548491 | 0.0546809 | 12567.4 | 0.0000327 | 0.95 | 0.0476639 | 0.0620221 |
| St. Bride’s crypt (known age) | 1740 | 1853 | M | 1.0002073 | 1.0007301 | 63.6024120 | 63.6337709 | 63.7592027 | 32254.3 | 0.0081643 | 0.95 | 60.6589371 | 66.4269445 |
| St. Bride’s crypt (known age) | 1740 | 1853 | rate | 0.9999985 | 1.0000287 | 0.0100125 | 0.0100126 | 0.0100097 | 119697.3 | 0.0000003 | 0.95 | 0.0098169 | 0.0102088 |
| St. Bride’s crypt (estimates) | 1740 | 1853 | alpha | 1.0004308 | 1.0015894 | 0.0034406 | 0.0033730 | 0.0032441 | 14094.3 | 0.0000063 | 0.95 | 0.0020379 | 0.0049290 |
| St. Bride’s crypt (estimates) | 1740 | 1853 | beta | 1.0008845 | 1.0032184 | 0.0491434 | 0.0491562 | 0.0493642 | 11007.9 | 0.0000520 | 0.95 | 0.0384382 | 0.0598310 |
| St. Bride’s crypt (estimates) | 1740 | 1853 | M | 1.0000909 | 1.0001930 | 66.5116525 | 66.3845608 | 66.2563248 | 35656.6 | 0.0160904 | 0.95 | 60.7073912 | 72.6176158 |
| St. Bride’s crypt (estimates) | 1740 | 1853 | rate | 1.0000276 | 1.0001275 | 0.0099942 | 0.0099897 | 0.0097761 | 42873.4 | 0.0000121 | 0.95 | 0.0050317 | 0.0148290 |
# get symbols & colors from palette alphabet (max n = 26), alt. glasbey (32), polychrome(36)
plotcolors<-palette.colors(palette = 'alphabet')
plotsymbols<-c(17,18,15)
# MOLA Welcome data without correction of population growth
english_wellcome <- rbind(english_mortality_prep, wellcome_prep)
# slight modifications
english_wellcome <- english_wellcome %>%
mutate(data = factor(data, levels = unique(data))) %>%
mutate(source = gsub('written','England & Wales written', source)) %>%
mutate(source = gsub('osteological','London osteological', source)) %>%
mutate(source = ifelse(data=="London 1728-1840","London written",source)) %>%
mutate(source = factor(source, levels = c('England & Wales written', 'London written',
'London osteological'))) %>%
mutate(start = as.numeric(start)) %>%
mutate(end = as.numeric(end)) %>%
mutate(year = ifelse(is.na(year), (start + end)/2, substr(year, 2,5))) %>%
mutate(year = as.numeric(year))
ggplot(english_wellcome, aes(x = year, y = M, colour = data, shape = source) ) +
ylab("modal age & HDI low - HDI high") +
xlab("year (from - to)") + ylim(2, 75) + theme_light() +
scale_color_manual(values=unname(plotcolors)) +
scale_shape_manual(values=plotsymbols) +
geom_smooth(color = "dark grey", method = 'loess', formula = 'y ~ x') +
geom_errorbar(aes(ymin = HDIlow, ymax= HDIhigh), width=0, colour = "dark grey") +
geom_errorbarh(aes(xmax = start, xmin = end, height = 1)) +
geom_point(size= 2 ) +
guides(size = "none",colour=guide_legend(ncol=1)) +
scale_x_continuous (breaks = seq(1200, 1800, by = 200)) +
theme(legend.position="none") -> english_wellcome_plot
# MOLA Welcome data with correction of population growth (_r)
english_wellcome_r <- rbind(english_mortality_prep_r, wellcome_prep_r)
# slight modifications
english_wellcome_r <- english_wellcome_r %>%
mutate(data = factor(data, levels = unique(data))) %>%
mutate(source = gsub('written','England & Wales written', source)) %>%
mutate(source = gsub('osteological','London osteological', source)) %>%
mutate(source = ifelse(data=="London 1728-1840","London written",source)) %>%
mutate(source = factor(source, levels = c('England & Wales written', 'London written',
'London osteological'))) %>%
mutate(start = as.numeric(start)) %>%
mutate(end = as.numeric(end)) %>%
mutate(year = ifelse(is.na(year), (start + end)/2, substr(year, 2,5))) %>%
mutate(year = as.numeric(year))
ggplot(english_wellcome_r, aes(x = year, y = M, colour = data, shape = source) ) +
ylab("modal age (corrected for population growth)") +
xlab("year (from - to)") + ylim(2, 75) + theme_light() +
scale_color_manual(values=unname(plotcolors)) +
scale_shape_manual(values=plotsymbols) +
geom_smooth(color = "dark grey", method = 'loess', formula = 'y ~ x') +
geom_errorbar(aes(ymin = HDIlow, ymax= HDIhigh), width=0, colour = "dark grey") +
geom_errorbarh(aes(xmax = start, xmin = end, height = 1)) +
geom_point(size= 2 )+
guides(size = "none",colour=guide_legend(ncol=1)) +
scale_x_continuous (breaks = seq(1200, 1800, by = 200)) -> english_wellcome_plot_r
# get the legend and remove it afterwards
ewp_legend <- get_legend(english_wellcome_plot_r)
english_wellcome_plot_r <- english_wellcome_plot_r + theme(legend.position="none")
# build the image
grid::grid.newpage()
ewp<-plot_grid(english_wellcome_plot, english_wellcome_plot_r, ncol=1)
modal_ages_plot <- plot_grid(ewp, ewp_legend, ncol = 2, rel_widths = c(.75, .25))
# Save the finished map object
ggsave(
filename = "fig06_modal_ages_plot.pdf",
width = 11, height = 8.5,
plot = modal_ages_plot,
device = "pdf",
path = "documented"
)
plot(modal_ages_plot)
The following data overview is build during pre-processing in ./chapter_04_results/Wellcome_DB.R and saved to a textfile (sep = \t).
kable(wellcome_overview_all) %>%
kableExtra::kable_styling(latex_options = c("HOLD_position","scale_down"))
| cemetery | beta | beta_range | M | M_range | ex20 | ex25 | r_beta | r_beta_range | r_M | r_M_range | r_ex20 | r_ex25 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Bermondsey Abbey | 0.0414 | 0.0319-0.0504 | 42.6 | 34.7-48.4 | 25.5 | 22.7 | 0.0439 | 0.0337-0.0529 | 46.3 | 38.9-52.2 | 27.1 | 24.1 |
| Bow Baptist Church | 0.0345 | 0.026-0.0429 | 32.6 | 20.4-39.4 | 22.7 | 20.4 | 0.0410 | 0.0318-0.0497 | 44.4 | 37.3-50.4 | 26.9 | 24.0 |
| Chelsea Old church | 0.0422 | 0.0328-0.0518 | 50.7 | 44-56.1 | 30.4 | 27.3 | 0.0458 | 0.0348-0.0557 | 55.3 | 48.9-61.2 | 33.1 | 29.6 |
| New Churchyard | 0.0365 | 0.0299-0.0432 | 22.5 | 13.7-27.9 | 17.0 | 15.0 | 0.0398 | 0.0331-0.0467 | 28.3 | 21.1-32.9 | 18.5 | 16.3 |
| Sheen’s burial ground | 0.0350 | 0.0263-0.0447 | 41.6 | 29.6-49.1 | 27.3 | 24.6 | 0.0407 | 0.0305-0.0508 | 51.1 | 42.6-58.3 | 31.3 | 28.2 |
| St. Benet Sherehog | 0.0353 | 0.0265-0.0446 | 36.1 | 23.6-43.3 | 23.7 | 21.2 | 0.0378 | 0.0283-0.0473 | 40.3 | 29.6-47.5 | 25.4 | 22.7 |
| St. Bride’s crypt (estimates) | 0.0455 | 0.0377-0.0547 | 60.0 | 55.4-64.7 | 36.8 | 33.2 | 0.0494 | 0.0384-0.0598 | 66.3 | 60.7-72.6 | 41.2 | 37.3 |
| St. Bride’s crypt (known age) | 0.0491 | 0.0423-0.0565 | 59.4 | 55.5-62.5 | 35.7 | 32.0 | 0.0547 | 0.0477-0.062 | 63.8 | 60.7-66.4 | 38.4 | 34.5 |
| St. Bride’s lower churchyard | 0.0511 | 0.0424-0.0599 | 53.5 | 50.2-56.6 | 31.0 | 27.5 | 0.0577 | 0.0483-0.0669 | 58.8 | 55.3-62.9 | 34.6 | 30.7 |
| St. Mary Graces | 0.0349 | 0.0267-0.0427 | 29.1 | 17.8-36.2 | 20.8 | 18.6 | 0.0372 | 0.0288-0.0455 | 34.1 | 24.1-40.4 | 22.2 | 19.8 |
| St. Mary Hospital, 1120-1200 | 0.0366 | 0.0289-0.0437 | 23.6 | 12.9-29.7 | 17.4 | 15.4 | 0.0382 | 0.0304-0.0454 | 26.3 | 16.8-32.3 | 18.0 | 15.9 |
| St. Mary Hospital, 1200-1250 | 0.0355 | 0.0289-0.0424 | 17.8 | 7.7-24.3 | 15.7 | 13.8 | 0.0399 | 0.0328-0.0467 | 26.3 | 18.9-31.4 | 17.4 | 15.3 |
| St. Mary Hospital, 1250-1400 | 0.0577 | 0.0529-0.0634 | 32.0 | 30-33.6 | 16.0 | 13.4 | 0.0608 | 0.0556-0.0665 | 33.8 | 31.7-35.6 | 16.5 | 13.8 |
| St. Mary Hospital, 1400-1539 | 0.0374 | 0.0307-0.0443 | 22.2 | 13.7-27.8 | 16.7 | 14.7 | 0.0400 | 0.0329-0.0467 | 25.9 | 18.8-31.3 | 17.4 | 15.3 |
| St. Mary and St. Michael | 0.0405 | 0.0323-0.0482 | 31.7 | 24.2-37 | 20.0 | 17.6 | 0.0460 | 0.0378-0.0542 | 41.1 | 35.7-45.5 | 23.4 | 20.6 |
| St. Marylebone | 0.0423 | 0.0331-0.0508 | 41.4 | 34.4-46.1 | 24.5 | 21.7 | 0.0452 | 0.0358-0.0541 | 45.5 | 39.4-50.5 | 26.7 | 23.7 |
| St. Marylebone Paddington Street north | 0.0486 | 0.0399-0.0578 | 45.0 | 40.2-49 | 25.4 | 22.4 | 0.0538 | 0.0448-0.0633 | 50.6 | 46.3-54.8 | 28.8 | 25.4 |
write.table(wellcome_overview_all, file = "./documented/table02_osteological_estimates.txt", sep="\t", quote = FALSE)
Data are hard coded in the code. Sources: Miles, Powers, et al. (2008), 97–103 table 32 (St Marylebone); Henderson et al. (2015), 81 (St Marylebone north of Paddington street)
source("./lifetables_processing/Marylebone.R")
kable(Marylebone_ranges, caption = "St Marylebone, corrected with population growth rate of 2.75 per-cent.") %>%
kableExtra::kable_styling(latex_options = "HOLD_position")
| parameter | modes | HDI.ranges |
|---|---|---|
| Marylebone beta | 0.0527 | 0.0433-0.0619 |
| Marylebone M | 54.4880 | 49.6-59.3 |
| Marylebone north beta | 0.0593 | 0.0499-0.0685 |
| Marylebone north M | 55.3931 | 51.4-59.9 |
The following plot is build in
./lifetables_processing/stbrides_crypt.R within the if-statement on
runCodeNew (s. data limitations above).
plot(stbrides_crypt_plot)
if (runCodeNew){
set.seed(3673)
lt_sim_list <- list()
for(k in 1:4) {
lt_sim <- lt.MC.Gomp(pop_start = c(10000, 1000, 500, 200, 100),
pop_inc = c(-0.02, 0, 0.005, 0.01, 0.02),
years = 200,
obs_start = 150,
obs_end = 200,
beta = (k + 2)/100,
bayes = TRUE)
lt_sim_list[[k]] <- lt_sim
}
# saves results in Rda-object
save(lt_sim_list, file = file.path(".", saveFileDir, "lt_sim_list.Rda") )
}
load(file.path(".", saveFileDir, "lt_sim_list.Rda") )
lt_sim_plot_list <- list()
for (i in 1:4) {
lt_sim_plot_list[[i]] <- ggplot(lt_sim_list[[i]], aes(y = surv_Gompertz_shape, x = as.factor(pop_inc))) +
geom_boxplot() +
ggtitle(paste0("\u03B2: ", (i + 2)/100) ) +
ylab("Gompertz \u03B2 (MLE)") + xlab("population increase") +
theme(plot.margin = unit(c(0,0.5,0.5,0), "cm"),
plot.title = element_text(size = 12),
axis.title = element_text(size = 10),
axis.text = element_text(size = 8)) + theme_light()
lt_sim_plot_list[[i + 4]] <- ggplot(lt_sim_list[[i]], aes(y = bayes_gomp_b, x = as.factor(pop_inc)) ) +
geom_boxplot() +
ggtitle(paste0("\u03B2: ", (i + 2)/100) ) +
ylab("Gompertz \u03B2 (Bayes)") + xlab("population increase") +
theme(plot.margin = unit(c(0,0.5,0.5,0), "cm"),
plot.title = element_text(size = 12),
axis.title = element_text(size = 10),
axis.text = element_text(size = 8)) + theme_light()
}
lt_sim_plots <- gridExtra::grid.arrange (grobs = lt_sim_plot_list, ncol = 4,
top = textGrob("Original Gompertz\n",
gp=gpar(fonsize = 14)))
# Save the finished map object
ggsave(
filename = "fig08_lt_sim_plots.pdf",
width = 11.5, height = 8,
plot = lt_sim_plots,
device = cairo_pdf,
path = "documented"
)
The chapter ‘Supporting information’ provides details about the London cemeteries included in the study, the Gompertz parameters of the Coale & Demeny life tables, and the simulations and their results.
Calculation of the lowest \(\beta\)-value for any of the Coale & Demeny life tables (Coale & Demeny (1983)) which is 0.0391 (the female table “West”, level 1).
source("./chapter_supplement/coale_demeny_life_tables_gompertz.R")
min(gompertz_df$Gompertz_shape)
## [1] 0.03913138
source("./chapter_supplement/simulations_run.R")
gridExtra::grid.arrange(grobs = plot_list_shapes, ncol = 3)
source("./chapter_supplement/simulations_run.R")
gridExtra::grid.arrange(grobs = plot_list_diff, ncol = 3)
# table of RMSEs
kable(rmse_result[order(rmse_result$RMSE) ,]) %>%
kableExtra::kable_styling(latex_options = "HOLD_position")
| method | RMSE | NAs | |
|---|---|---|---|
| 11 | Bayes (5y-cat) | 0.0045054 | 0 |
| 10 | Bayes | 0.0045342 | 0 |
| 7 | MLE | 0.0047464 | 0 |
| 4 | survival | 0.0047465 | 0 |
| 12 | Bayes (10y-cat) | 0.0048206 | 0 |
| 8 | MLE (5y-cat) | 0.0048251 | 0 |
| 5 | survival (5y-cat) | 0.0048980 | 0 |
| 1 | OLS | 0.0049008 | 545 |
| 9 | MLE (10y-cat) | 0.0051441 | 0 |
| 2 | WOLS | 0.0060401 | 0 |
| 3 | WNLS | 0.0061083 | 14 |
| 6 | survival (10y-cat) | 0.0067095 | 0 |
source("./chapter_supplement/simulations_run.R")
gridExtra::grid.arrange(grobs = plot_list_estim_shapes, ncol = 2)
# table of RMSEs
kable(rmse_estim_result[order(rmse_estim_result$RMSE) ,]) %>%
kableExtra::kable_styling(latex_options = "HOLD_position")
| method | RMSE | NAs | |
|---|---|---|---|
| 6 | Bayes (cat) | 0.0099026 | 0 |
| 7 | MLE_wo_OL | 0.0202114 | 71 |
| 1 | OLS | 0.0243214 | 442 |
| 3 | WNLS | 0.0293842 | 73 |
| 2 | WOLS | 0.0328083 | 2 |
| 5 | MLE (cat) | 0.0761568 | 0 |
| 4 | survival (cat) | 0.4731442 | 0 |
#source("./chapter_supplement/simulations_run.R")
gridExtra::grid.arrange(grobs = plot_list_bayes_diff, ncol = 2)
source("./chapter_supplement/bayes_complete.R") # can take a few minutes
kable (bayes_complete) %>%
kableExtra::kable_styling(latex_options = c("HOLD_position","scale_down"))
| mode | thinning | steps | parameter | PSRF Point est. | PSRF Upper C.I. | Mean | Median | Mode | ESS | MCSE | HDImass | HDIlow | HDIhigh |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| known_age | 1 | 10000 | a | 1.003210 | 1.006108 | 0.0028582 | 0.0028441 | 0.0027725 | 462.7 | 0.0000154 | 0.95 | 0.0022403 | 0.0035193 |
| known_age | 1 | 10000 | b | 1.001893 | 1.003920 | 0.0480363 | 0.0480265 | 0.0481745 | 488.6 | 0.0000947 | 0.95 | 0.0440097 | 0.0520917 |
| known_age | 1 | 10000 | M | 1.001259 | 1.003216 | 73.8375371 | 73.8501409 | 73.6934420 | 930.5 | 0.0357533 | 0.95 | 71.6915433 | 75.9608132 |
| known_age | 20 | 100000 | a | 1.000011 | 1.000109 | 0.0028495 | 0.0028327 | 0.0027934 | 71982.2 | 0.0000013 | 0.95 | 0.0022163 | 0.0035260 |
| known_age | 20 | 100000 | b | 1.000005 | 1.000090 | 0.0480993 | 0.0480962 | 0.0483082 | 71181.0 | 0.0000080 | 0.95 | 0.0438344 | 0.0521777 |
| known_age | 20 | 100000 | M | 1.000000 | 1.000078 | 73.8543153 | 73.8768307 | 73.9884330 | 84071.3 | 0.0037849 | 0.95 | 71.6339091 | 75.9294081 |
| estimation | 1 | 10000 | a | 1.007384 | 1.023678 | 0.0028312 | 0.0028026 | 0.0027942 | 167.5 | 0.0000382 | 0.95 | 0.0019049 | 0.0038193 |
| estimation | 1 | 10000 | b | 1.011691 | 1.038693 | 0.0510970 | 0.0508290 | 0.0503803 | 86.5 | 0.0005942 | 0.95 | 0.0404465 | 0.0624583 |
| estimation | 1 | 10000 | M | 1.005548 | 1.017117 | 71.9242579 | 71.9119671 | 72.0531786 | 392.2 | 0.1119194 | 0.95 | 67.6950056 | 76.3291669 |
| estimation | 20 | 100000 | a | 1.000247 | 1.000941 | 0.0027769 | 0.0027509 | 0.0027034 | 29177.9 | 0.0000026 | 0.95 | 0.0019290 | 0.0036726 |
| estimation | 20 | 100000 | b | 1.000354 | 1.001342 | 0.0516959 | 0.0514776 | 0.0502964 | 20843.0 | 0.0000356 | 0.95 | 0.0421542 | 0.0619696 |
| estimation | 20 | 100000 | M | 1.000091 | 1.000334 | 71.8362699 | 71.7754410 | 71.6155191 | 45976.8 | 0.0102799 | 0.95 | 67.6297829 | 76.2104655 |
Institute for Prehistoric and Protohistoric Archaeology - Kiel University nils.mueller-scheessel@ufg.uni-kiel.de↩︎
Institute for Prehistoric and Protohistoric Archaeology - Kiel University, k.fuchs@ufg.uni-kiel.de↩︎
Institute for Prehistoric and Protohistoric Archaeology - Kiel University, crinne@ufg.uni-kiel.de↩︎